Got a chance to settle down with this a bit and do some coding.
AT failure to update contained strength bug --
SOLVED.I found the last piece of the puzzle while I was pulling together a reference list to keep handy while I worked and corrected the minor error in logic that was blocking ATs from realizing they needed to update if their contents went from something to nothing. Fixing this would produce a small increase in extra work on the system as transport-class objects are no longer blocked from checking their contents' strength and count if the number contained is 0, but as they are empty, this should be a trivial effect. I noticed no performance loss in testing.
Confirmed carriers wouldn't be affected as they can never cycle through contents from something to nothing back to something in the same object, since they self-destruct on hitting 0 contained ships.
Barracks have similar logic to ATs but probably not affected as I don't think I have ever seen one empty unless it was in the process of being destroyed or self-destructing on planet ownership change.
Incidentally, I discovered another thing I love about this game, if it throws errors it screams them not only out into the log, but into the message log in game. I don't even have to alt-tab back and forth to see if I blew something up that didn't manage to take the game down. It's so... practical. <wipes away a tear of dev joy>
Now that I have a debugged base for ATs, time to move on to the fun stuff of messing with their damage and abilities.