Quite honestly, I think a lot of **** got left in because, by the time we really got to cranking on the rules for ships, we were half way through the playtest...
Starship combat got really hosed; we'd been tweaking the system (Hunter was excellent at addressing concerns, even if he did occasionally show some well earned ire at some of us...) a lot, and finally had an excellent ballance, but then at the last bit, and due to near-universal griping, it was decided to double the XP rates... which added another 2-4 levels per character, and unbalanced a lot.
The limits were left in originally to keep backwards compatibility. But later changes came, and made certain bits less than desirable, and nearly senseless; the no bays matching your spinals being a prime case in point. It quite simply got overlooked, and probably should have gone the way of the Dodo, but that's hunter's call for 2nd ed...
I think a HG baseline was the way to go, but all the restrictions should have been dropped from the text, and then added back as needed. Then again, it was planed up until near the end to have that USP from HG in the book, too. Dropping the USP deleted the need to have the restriction on matched bays and spinals, but they survived as an artifact... boy those were hectic times for the playtest.