Bingmann tested it soundly, although it might have been in SMACv4.
He reported there weren't ANY differences in the repair rate with or without bays, under any possible conditions.
I see that you raise many doubts and pose many questions.
You'r doing a good investigating job.
I guess you could put up a simple scenario and perform some tests on your own, if you're not doing it already of course ;^)
From time to time I still do, as I still left many game aspects for granted, despite my fame here