I can tell you for sure that nothing exists that will do what you want the way you want to do it. No SNES emulator, for the PC or otherwise, emulates the features of the Super Gameboy pass through cartridge. The Super Gameboy itself contained gameboy hardware (modified z80 cpu, and what not) in the cartridge and just passed information to the SNES.
No SNES emulator author has taken the time (wasted the time) to do so when adequate Gameboy emulators are available that have Super Gameboy features.
Now as for how to get Super Gameboy/Color Gameboy games to work on a Gameboy Micro flash cart, I am not familiar with.
_ _ - - = = Pr3tty F1y = = - - _ _