1) Sure. There are plenty of patches for Japanese versions of games and if someone decides to use another region as a base (more space, more features, less bugs, because why not....) it is all good. Given the choice you would be encouraged to pick the more popular one but again reasons for not doing that can be "why not" if you want.
2) This is a long standing point of discussion. The short version is you are going to need to make a patch to apply to the patched ROM, which is to say patch the original ROM with the hack you want to use as a base and then make a patch to go from that patched ROM to your hack. Annoying, maybe but it is what people decided. You see similar things elsewhere where I might not modify an archive for a program but I can include the original archive in my new archive just fine.
3) Does it work on hardware, or could it work on a reasonable hypothetical flash cart (some SNES carts do not run a handful of games that have certain extra chips that current flash carts do not support but it is an accepted chip that someone could emulate later with some extra hardware, however it is not like someone invented a crazy extra chip/mapper or bolted on a crazy CPU and made a ROM run on it)? It is poor form but if a hack say does not fix a header that an emulator might ignore but get past that and you are good then it is not going to get you troubled.
It would also include things like high definition texture replacement and texture swapping hacks like we see sometimes for the N64, GC and Wii. HD texture replacement/addition is fairly obvious but the other sees people tell the emulator to swap out textures (which owing to the way a lot of 3d systems work means the 2d UI as well) in an effort to translate the game. For most around here it is an insane way of setting about hacking such things as the patches often end up in the gigs, might not account for branching story, obviously don't work on hardware and more besides but it does reduce the barrier to entry to can install GIMP rather than all the things covered in http://www.romhacking.net/start/
It is another contentious issue but the people here take the long view and emulator bugs get fixed, new platforms get opened up (see for instance all those having android as their primary computing platform), hardware is good (even the N64) and playing to hardware and not using bugs means everybody has a level playing field.
Where this leaves lua scripts for emulators is a different matter, however you would probably be encouraged to submit those as a document or something.
There is always scope for design to sway things that might not go otherwise -- nobody cares if Sonic is now green as you changed a palette somewhere, however if it turns out that is makes it more playable (or playable to someone that is colourblind) then fewer people would object and those would probably be overruled.