A/UX will run perfectly happily off a “virtual” scsi2sd disc. That is how my installation is set up: multiple virtual devices for a recovery disc, two MacOS versions and A/UX. Never tried it on a IIfx, mind, but it ought to work.
Mostly a combination of the Macintosh Classic schematic (a cost reduced SE that also uses the same BBU), and backtracing pins on the board. Sprint has this wonderful 'test' feature - click on any pin of the BBU, and you can see exactly where it goes. I'll send you the sprint layout file if you like, you can take a look yourself.