@Minim: can you remind me where you are downloading the NeoLemmix conversion you looked at, so I can check things out for myself? Also, do you think your post above (and then my reply here) might be better suited moved to Proxima's "
NeoLemmix versions of original levels for challenges" topic?
Thanks for the due diligence.

Regarding for the examples you mentioned so far, I've checked the original levels in Lemmix level editor, and would eventually like to see the same NeoLemmix levels you were looking at to compare. With that in mind, comments so far (w/o seeing the actual NeoLemmix levels):
edit: in process of updating replies here, now that I've actually had a chance to look at the NeoLemmix levels in question. Updated sections will be marked [updated]. Sections not yet updated should be disregarded for now, as they may not actually reflect the reality of the NeoLemmix levels in question. Sorry for the confusion.Sunsoft 16
[updated]Huh, that's an interesting arrangement, didn't notice the very irregular treatment they've done with the steel. It's really hard to tell visually whether there's actually a gap in the steel and whether it can be breached with sufficient fencer uses.
Personally I'm leaning towards just having regular, fully square steel blocks there matching the steel areas in the original level (ie. resulting in no breachable gaps). Admittedly that will kill off the level for new-skills challenge (not involving extreme utilization of nuking).
But I'm not really opposed to the other way either. I'm now more convinced to change it to regular, fully square steel blocks and not allow the possibility of breaching through that small gap. It's not possible in the original (since the steel areas fully cover that part of the level), but with the given skills, the gap in NeoLemmix definitely looks exploitable, and at the same time I don't get a strong sense that there was ever any intent for breaching through that area to be a viable solution.
Mayhem 2 "The Boiler Room" is another annoying example. It has steel pixels guarding the exit pillar and inside the blue wall.
[updated] Interesting find! So apparently, it looks like the level designer used the steel plate graphics to fill up the natural tiny dents in the pillar and the wall in question, so that it's perfectly vertical without dents. Technically bits of steel plates are exposed through the dents being filled, but the intent is clear, they were never meant to be real steel (and had no steel areas in the original level, obviously). The rest of steel that's obscured by the pillar/wall graphics remain non-steel as intended.
This needs to be fixed. Thankfully I believe it's easy enough to do so by replacing the use of steel plates with, say, the gray circle terrain graphic, to perform the same job of filling up those tiny dents.
Fun 24/Mayhem 3 is an unusual one. It has a steel "Tongue" lurking beneath the floating platform near the bottom.
[updated] Good eye!

It was really hard to spot even in CPM thanks to its poor choice of colors for terrain vs steel.

There is no tongue of any kind in the original because the steel areas actually don't align perfectly with terrain (as is typical, due to the multiples-of-4 technical requirement). In the original level the entire bottommost row of pixels of the floating pool are terrain (ie. not covered by the steel areas), even though their pixels do all come from the steel plates.
While I agree the "tongue" is really tiny and at a location that's probably not very exploitable, it's really weird to be there and should be fixed. Given how small it is, I don't believe it'll be hard to get rid of the tongue.
It's also ironically a prime counterexample to the current system's supposed virtue (not that I'm opposed to it, but counterexamples like this needs to be highlighted nonetheless, to illustrate it's not always that simple). The system presumes that what-you-see-is-what-you-get and therefore more honest. But I'd wager that no human eyes would've spotted that tiny tongue of apparently exposed steel there without help from CPM. So for most people what they
think they see is not quite actually what they are getting.
Fun 27/Taxing 22: The steel beneath the starting platform is overwritten by slime.
[updated]Thanks to the acid, I'm reasonably sure there is no meaningful exploit of the steel being no longer extending all the way to the bottom. That said, as a side effect that does open the possibility of exposing the right edge of the acid object via terrain removal, though that's not something you'd naturally do for any typical challenge solutions.
So I can go either way, and laziness suggests leaving it as-is.
Fun 29/Mayhem 9 & Mayhem 28: Steel overlapped diagonally by the pyramid and past the exit platform respectively, but because it's so visually obvious, we should leave these ones.
[updated]Agree, let's leave those as-is, especially for the pyramid in Fun 29/Mayhem 9.
Mayhem 8: Steel bits lurking right above and to the right of the exit platform, but it's a clear path to the exit so.
[updated]Interesting. Obviously no functional steel areas there in the original level. The steel are barely visible, and clearly the level designer was merely exploiting the few exposed red pixels of the left/bottom edges of the steel plates, in order to simulate the effect of a red glow of the exit's flames against the gray rocks.
I'd almost go as far as examining whether to try replacing all the steel plates there with other terrain (plus eraser pieces) to end up with the exact same pixels color-wise to get the same visual effect, but without using any steel plates, so that there is no odd-looking functional steel there at all. That said, the amount of exposed and therefore functional steel is so small, it's unlikely to be exploitable for anything, so probably fine to leave them all in?
Tricky 9/Mayhem 6: Steel overlapped on the left edge.
[updated]That's quite isolated and out of the way. Seems fine to leave it as-is (so the rocks remove the functional steel where it overlaps), it seems preferable visually, compared to making the entire steel plate be drawn on top of the rocks.
Mayhem 12 & Taxing 21: Left sides particularly.
[updated]I can go either way with Mayhem 12, even visually, since most of the steel in the level (except for the area you noted) are actually drawn fully on top of rocks. It's another case where the overlapping terrain removing some of the steel doesn't seem very exploitable so leaving as-is seems fine, though it's not so clear in this case whether even visually it matters.
As for Taxing 21, it's really hard to imagine that tiny bit of overlap is intended even visually, it really feels like the level designer forgot to set no-overwrite to the non-steel to keep it behind the steel plate. I'm inclined to fix it so it doesn't take out any of the steel, just like there's no irregularities in the original level with steel areas.
Mayhem 15/Tricky 10: A few pixels from the left steel block are overlapped, but lemmings can't access this thanks to the fire's trigger area
[updated Interesting, so apparently the steel plate on the left pillar is misaligned one pixel to the left. Normally for any other purposes I would move the steel block one over, but for challenge purposes I'm tempted to leave the misalignment as-is so it matches how the level really was in the original.
In the original, the steel area nevertheless still extends past the full width of the pillar. To preserve that in NeoLemmix while also preserving the misalignment of the steel plate, I'm considering adding a second steel plate there (behind the one that's already there, but in front of the pillar's terrain)
The little bit of terrain that actually ate away a tiny part of the steel plate, that seems like a mistake to me given an almost identical setup is done for the stuff between the middle and right pillars, but in that setup the terrain remains fully behind the steel and does not affect it. I'd want to fix it.
Taxing 16 & 24: Some of the steel on the ramp is overwritten. Also for 24: The water beneath the chains is off-centre by a pixel to the left.
Tricky 28: Right side "platform"
Sounds like yet more cases of NeoLemmix not respecting no-overwrite with its handling of steel plates overlapping with other terrain. In the original all the steel plates in question are fully visible and not obscured by any other terrain as far as I can tell.
Fun 21/Mayhem 26
Seems ok and not very exploitable to let the terrain remove some of the functional steel. I also see some steel-plates-used-as-eraser-pieces which shouldn't be treated as functional steel.
Finally, interestingly in the original level, there is a bare steel area (ie. not overlapping with any actual steel plates) spanning from left of the bridge all the way past the exit). I believe it's there to (try to) prevent the player from bombing out the terrain resulting in visually exposing the edges of the water object there. (Although given the original game's poor steel handling, I'm pretty sure you can still set things up to bomb away enough terrain to expose the water object's edges, despite the added steel areas.) There's no good way to put visual steel plates there to achieve that function in NeoLemmix without adversely affecting the visuals, so I think I'd rather leave it as-is with no steel there in NeoLemmix, even if it means you can, indeed, bomb out terrain and expose the edges of the water object.

Mayhem 18
Taxing 2
Again, a quick glance looks ok to leave things as-is and let terrain remove some of the functional steel.
Tricky 4/Taxing 7
The shape formed by the steel plates is a key visual element, so definitely should leave as-is, once all the mosses are removed so the "ship" isn't so full of cracks.

on Taxing 4 the trigger area for the right spikes trap doesn't overlap the wall unlike the one on the left, allowing climbers to climb all the way up. However, there are no climbers in this level anyway so not sure.
Actually, at least looking at the DOS version, the left trap's trigger is still 1 pixel away from the wall, so I think both walls are climbable (except for lack of climbers given to the level). That said, it does feel like this is begging for a slight adjustment in the traps' positions so their trigger areas do touch the walls.
Looking at the version you created a while back for the "new skills" challenge, it looks like you did fix the positions of the spike traps? However, I also noticed you replaced the spike traps with the smaller versions. While that would match the abnormally small trigger areas in DOS version, it should be noted that on SNES (and therefore probably Amiga, though I haven't tested yet), the regular "big" spike traps do have larger trigger areas that are more in line visually with the spikes. It seems NeoLemmix had also fixed the large spike traps so their trigger areas basically match Amiga versions. So I'd say we shouldn't replace the spike traps with the "small" versions. The abnormally small trigger area in DOS is arguably a bug, it's certainly misleading relative to the visuals of the spikes.