The other option is to drop the idea of a 2.5" form factor altogether, and use a CF adapter as you (and others) have suggested in the past. Do you have a current recommendation for which CF adapters are good to use in the Empeg? (For example
this one?)
Not that one -- it has a desktop drive style 40-pin connector. But pretty much any of them with a 44-pin 2.5" drive connector on them should work --> no electronics involved
other than a 3.3V regulator. The CF cards _are_already_ native IDE/PATA by design.
You're saying the builder image just sticks a bash script in flash memory and runs it from there?
That script _is_ the bigdisk builder.

Plus a little bit of minor other stuff in the .upgrade file (flash partitions) that the emplode/upgclient re-flashes each time --> mostly unnecessary, but it does include the Hijack kernel zImage file, and the upgclient also creates the basic drive partition table.
The script, and supporting libraries/binaries, are written by the upgclient to /dev/hda5 (root partition), and then the builder reboots into that system to run the script to do the rest.