Why aren't the transport bays on Small Craft (and other non-capital units capable of mounting bays) counted when evaluating the transportation of a force? My understanding is that they are equivalent to the bays that are counted, and they ultimately require the same amount of space.
For a specific example: I'd like to design a transport DropShip with Small Craft bays rather than Battle Armor bays: the Small Craft themselves contain battle armor bays, which allows the battle armor in transit to be deployed for boarding actions and such if a fleet is intercepted.
This arrangement seems to show up in-universe, such as with the NL-45. And the entire point of using a bay over a compartment is including permanent accomodations (including support personnel), so it can't be a matter of not being suitable for long-term travel.
I suspect this rule was added to ensure a company actually has the ability to make jumps with all of their bays. If so, I'd appreciate a simple modification: if enough Small Craft bays are present on DropShips/JumpShips/WarShips, all bays within the Small Craft are counted for the purpose of the Company Rating.