With a homebrewed 3DS, you can inject GBA games onto your 3DS homescreen as Virtual Console titles. I don't think it's technically emulation, but it's also obviously not a physical game cart plugged into a GBA/NDSL, so I figure I should double-check before possibly breaking the rules by using an unacceptable method of running the game.

Are they allowed, and what would I submit it as if it is?

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