I actually ran the program under Mini vMac in Windows to generate the screenshot.
Yeah, you still need an external EPROM programmer to do the initial programming of the flash chips - you can't just stick blank ROMs in the computer and boot it up. But once the ROM has been programmed once, you can use this Flash Tool to update its contents without removing the chips from your Mac. If you could get a friend to do the initial programming for you, or buy pre-programmed chips, then in theory you wouldn't need an external EPROM programmer at all. But techknight's right about the risk of some unexpected error writing bad data to the code section of the ROM, essentially bricking the Mac until you reprogrammed the flash chips externally.
I looked into it a little, and I don't think it's possible to extend the ROM area beyond 1 MB without multiple hardware and software changes. In theory it's probably doable, but not really worth the effort. 1 MB is a good number.
But maybe someday...