That won't work; the flasher program is a tiny thing that pipes the image in via commslink. As for the odd size, the actual firmware occupies 64KB, the rest is the stock code list, and the rest of the flash is used for additional codes and copied saves. I've looked into disc-hosted flashing a bit but need to leave for work about 2 minutes ago, so bug me about it on IRC or PM or whatever and I'll see if I can get something going later tonight.
edit: didn't see your hypothesis on the flash, actually the cart bus is 16-bit and the Saturn accesses it as one big chunk of flash similar to the way 8-bit EPROMs are wired on Genesis.