Just for fun, today I decided to see what would happen if you patched Pokemon Yellow to be a GB-strict ROM, rather than a GBC ROM.
Basically, it's the Gameboy Color emulator, but the game is in the standard, brownish grey monochrome of the Gameboy emulator. You cannot switch the screen to a green color, sadly.
TL;DR The GBC emulator can emulate Gameboy games as well, which is to be expected I guess.
A theory would be that the two are all in one emulator, and that it just picks the overlay and options based on what the ROM seems to be upon boot time. Knowing this, it gives in-sight that the patches are applied to the ROM after the emulator launches, but just a tiny bit before boot. I dunno, just a cool little thing I've observed.
On the subject of Mode2, using Link's Awakening DX's patch as a base, I'm no farther than before. I thought that the Fixcode variable might have been the magic key to all of this, but changing that within the patch does nothing. Perhaps Mode2 was STRICTLY changed just for Pokemon G/R/B/Y? The question would be, "why?"...