1. Save and quitting is allowed but you must go back into game immediately, the main reason it being allowed would be rng manipulation and saving before a fight that isnt a guaranteed win so you can soft reset and refight when you lose

2. You can use normal saves on emulator, Menu -> Save -> Soft reset or hard reset -> Save will be there for loading, if its not there for you, please make sure youre only using an approved emulator (newest mGBA) and that the folder its in is writable.

After doing some research on the topic, ultimately I would say this is not allowed.

I believe the main reason would be that, the unwritten rule of having to play on an original cartridge and the injected rom kind of sort of being cartridge reader emulation.

Also, I think the games may be or must be "SRAM patched" or optionally "Sleep patched" to function on the 3DS

The recommended choice is a Gamecube with a Gameboy Player w/ a gamesave exploit to run Swiss and Gameboy Interface, with a capture card

Or a GBA, GBASP, NDS, with a capture card or camera