I thought the main point of the fork was to play any level 100% classically
Yes, but there needs to be a way to implement the classic behaviour with a minimum of fuss. I believe that making all of the problematic situations impossible from a level creation point of view is the best way to go, all things considered.
and it can be quite frustrating if you don't know if you haven't figured out a solution or if it's impossible.
Well, that's the point - making those impossible situations impossible to
create means that those levels couldn't exist on the engine in the first place. So, there will be 0% chance of a player becoming frustrated because an impossible situation has been presented in their chosen bomber mode; it simply couldn't happen. In the absence of a better idea for fixing everything, this seems to be the best the way forward for now.
the skill shadow will show where the lemming will be in 5 seconds in timed mode.
Having given this some thought, timed bombers shouldn't have a skill shadow at all. It completely defeats the purpose of them being timed and is against the spirit of the proposed "classic" mode, for which timed bombers would be a standout feature.
If you hold down a hotkey and click a lemming in the first 5 seconds of it's existence it will bomb it instantly in timed bomber mode
Again, I've pretty much decided this won't be the case. Not allowing untimed bombers in the first 5 seconds is a far cleaner solution to all of the associated problems. We don't need the hotkey, or my proposed "hot bomber" state (which is admittedly an even messier solution). Far better to keep things simple where possible.
EDIT: Besides, if it's later agreed that the modes should be switchable in-game, this feature can always be added retroactively.
If you clone a bomber, hold down a hotkey to make the clone a bomber
The more I think about it I'm generally against hotkeys being needed for any sort of skill assignment. I'd rather remove the cloner skill altogether than make this sort of mess. Whilst it was me who originally floated the idea, admittedly, I did so for the purposes of discussion; a number of problematic situations have been presented, each of which seem to require hotkeys, menu-diving or other UI headaches in order to crowbar the timed bomber feature back into an engine which has clearly outgrown it. For me, the purposes of this discussion was to try and find the "solution of least resistance".
Thankfully, a relatively simple idea has come up which eliminates this need for hotkeys and other UI mess (which goes against the spirit of "classic" lemmings gameplay anyway). For now, I'll be going ahead with that unless an even better idea is suggested in the meantime.
Try to think up some solution to make NeoLemmix and SuperLemmix 100% compatible with this issue
(Pictured)
Not implementing a mode-switching hotkey solves this problem.
Just to re-iterate, breaking existing NeoLemmix levels is not a problem for me if this project does go ahead. NeoLemmix, Lix and SuperLemmini(Too) all feature levels which can't possibly be played on the other engines, either for physics reasons or game feature differences. I'd be absolutely fine with SuperLemmix being its own thing and thus having levels which aren't cross-compatible. If nothing else, it paves the way for it to take even bolder steps in the future (that is, if it ever exists!).
Therefore, existing-level-preservation will categorically not be a concern for me personally whilst I'm working on this (and that goes for my own levels as well!). Just thought I better make that clear at this point

I also thought I better mention that, if this project doesn't attract much support and if the ideas being discussed prove to be too far beyond my capabilities, I'll have to abandon it anyway. Let's keep it real at this point - SuperLemmix is just an idea, and I currently
have no idea how to do any of this!

Anyway, let's keep positive. I can certainly have a go at some of this and see how far I get. I've updated
the OP with the ideas as they currently stand; the decisions aren't entirely final by any means, but provide a way forward.