You can change layers with R and F (should be in the Help section in the pause menu)
The game was not intended for touch controls, it is something that i'm looking to try in the future so i can make an Android release too.
Puzzles don't really have a limit for the sides but max height/layers is 50. Still, keep in mind puzzles of that size can have a significant performance impact (i'm pretty sure it's due to the simplistic aproach i took).
The grid in the editor is purely visual and only really updates when loading a puzzle, main reason is that puzzle size does not have a set limit (aside from layers) so it would need to recheck the size every time you change a tile to update properly. It's a low priority thing rn.
I was working on a re-usable key remapper but i had difficulty integrating it into the options menu since it builds itself from your config file (and it's difficult to build itself from something like "buttons"). I was working on a different project, but when the remapper is ready for that one, i can port it to this game.
Same with other features, i'm planning on updating the buggy code with stuff from the new game when i have it.
Thanks for the feedback tho. I'm also glad the Linux version doesn't self destruct or anything.