Most mods don't overwrite, only the ones in the main game. Not having to overwrite anything when trying to alter something from the main game just ISN'T possible. I HAVE however once thought of making one small addition to the main game in Naija's cave, a doorway of sorts, that'll put you in a room that can be connected to dozens of mods.
So as to your questions, I'm not exactly sure why you're asking them here. Only Alec can answer them, which hasn't worked on the game in ages and has forgotten the code, or so he has said before. Besides that, if you have basic lua knowledge, wouldn't you know if it was possible, or at least know where to find lua tutorials?
The second question comes back to the first one, I'm not sure if it can do those actions. I mean, it DOES save the mods on which you are working on in the editor, but that code is deep in the game and probably not lua.
Third, on the fly? Probably, they need co-ords to be placed at, it could probably be that you can script a node to make them spawn, or of course, if you have them written in the xml map file. I'm not sure what you mean with "A map with bubbles for these new modes." though.
All in all, I more than appreciated this idea and hope you'll put it in the works.
Also if you weren't aware yet, the source of Aquaria has been released a while ago.
http://hg.icculus.org/icculus/aquaria/Sadly enough not a lot of people were interested in the game and handy enough with code to do anything. :C
