As talked about on stream:
The majority of the auton bay's functionality should be possible to have done (for a price) at auton dealerships (and possibly some other stations as well). This would include repair and replacement of armor, device installation and removal, renaming, and restoration of salvaged autons (for the edge case when someone grabs a destroyed auton via an auton bay, then gets rid of said bay before the auton is restored).
The auton bay would still have the advantage of doing this for free, on demand, identifying all autons when installed, and also allowing salvage of autons in the first place.
(This might be possible to re-use for managing companions' ships as well)