I think there used to be a Server Rule which stated that a player who used their own bounties as a means to circumvent ID limitations could be sanctioned. So if you run faction ABC- and your ID lets you treat bountied transports as combat targets, then you bounty faction XYZ- and start killing their transports without demands, you'd get in trouble. With that, you've essentially used a loophole to be able to kill transports left and right.
I just tried searching for this rule, but couldn't find it, so I'm not sure why/when it was removed, or if it even exited in the first place. Nonetheless, that's why [UC] doesn't let its members fulfill any of our internal bounties on transports, unless they're already bountied elsewhere. With no current standing rule (that I could find), it's now just a fair play consideration.