Decided to give this its own topic, since it doesn't really have anything to do with APT (previous posts were in the APT Hard Disk Preparation and Utilities thread).
Can't start it with a download quite yet (although there'll be a version to test in a day or two), but I wanted to demonstrate the basic procedure for editing the flash ROMs so people can hit the ground running when I post a version of the software for testing.
The video shows a PBI ROM update, followed by BASIC slot 2 being replaced by the Atari Assembler Editor. You'll notice the slot descriptions can be edited and flashed to ROM at any time. I then replace the High-Speed OS with the 1200XL OS.
Flashing is somewhat slower than it would be when using 4KB sector flash ROMs (Altirra only emulates 64KB sector chips for Ultimate), and of course it's also possible to load all ROM images from the hard disk (in the video, they're loaded from the host device via SIO).
Don't really want to spend too long on this, so hopefully it'll be done shortly. I need to add 4KB sector and Incognito support before I have something ready for testing.