Nice info there. I've been planning on removing the seperate supergb driver we have in MESS now and replace it with full snes+gb emulation so it can work more like the real thing did. But I have not done anything towards really adding it yet.
What I did notice is that after the initial sending the gameboy rom information the actual sgb games read back from ff00 and expect to not see the lowest 2 bits set. If both bits are set the games will not send any sgb games, otherwise they will. I don't think that explains anything about 6001 and 7800 though.