Thanks for the feedback.
After the last of our changes on Friday, we had an APU and ALIX running power cycles over and over in a loop while permanent rw mounted on the slowest SD/CF I could find. Each went through 1000 power cycles with no issue. IP PDUs are handy. :) Only certain cards seem to corrupt themselves easily in that circumstance. A SanDisk CF even with SU+J and permanent rw didn't break. The Kingston CF I used for the 1000 cycles never made it more than 2-3 power cycles left rw SU+J.
The last part on config writing is being tested right now. The basic case, making a config change and immediately pulling the power, was fine last week. The enclosing directory wasn't being fsynced though, which meant if you did something insane like write_config() in an endless loop called at startup and drop its power right in the middle of that loop, you could be left with a wiped out /cf/conf/backup/ because it overwrote the entire history in 1-2 seconds of the loop and that wasn't fsynced. If you hit the exact right (or wrong) moment, you could end up with a missing config, and no backups to restore. That's about a 1 in 200-300 tries occurrence where you're writing the config in a non-stop loop when power is lost, and probably impossible to encounter in any reasonable real world circumstance. But even that scenario should be fine now. Two systems running in a power cycle loop right now to confirm that. Leaving that running all night.