It will supprt EMS 64M, but only for one of the pages. It will in general not support GBA carts because GBA carts are using 3.3V power and old cartridges are using 5V power. A 3.3V chip may not tolerate those 5V, but if it can be determined that a certain GBA cartridge is 5V tolerant, there's not much stopping me from adding software support for flashing it. This might be a can of worms if people accidentally fry their GBA carts, though.
One solution would be to make use of some sort of adapter card that you plug in between the flasher and the GBA card that drops the power down to 3.3V and passes the rest though as a simple passive passthough.