Some thoughts:
If you're going to do this, it's quite clear that you don't really intend on following the existing NeoLemmix philosophy in regards to the player assist mechanics, and I'd have to question if it makes sense to appease both crowds with this engine. Perhaps fully embrace this engine's difference in philosophy and then design a cohesive experience around that. If we still want to maintain the existing philosophy, there's no reason we can't make divergent forks.
As part of this, rather than allowing levels to disable player assist features, I think it would be better for you to decide which player assist features this engine should keep. As a general rule, I'd suggest definitely keeping the player assist features that multiplayer Lix allows you to use:
- Directional Select. It only breaks one official level, and that one level has a trivial solution and is at worst a 1 in 8 chance to solve correctly if you don't even try to get the timing right. It prevents you from having to redo a level simply because, for example, you had to pick a lemming out of a crowd and you got unlucky (in practice, there's no RNG going on, but the way small differences can affect the exact alignment of lemmings may as well make it RNG). Additionally, a few of the official ports support it.
- Splat Ruler. Not even remotely game breaking even on levels with trivial solutions that are just finicky to pull off.
In addition, I recommend keeping Clear Physics Mode just because let's be honest hidden objects suck and it doesn't actually make fair levels easier.
The rest I'll refrain from commenting on for the time being. Though I do hope you at least keep pausing with a hotkey even if you don't keep assign while paused. There's precedent, lots of the official ports support it.
Why disable auto screen start? That's not a player assist feature, that's a designer assist feature. You leave auto screen start on and it chooses a sensible starting position for you, and then you override it in the editor if you don't like what it chose.