A few comments on the nature of the transport.
This is not a 'shuttle', this is an interstellar diplomatic transport. That's like saying a cruise liner is a dinghy, they do the same job, move people, but they have radically different profiles. If it is truly a 'civilian' ship it wouldn't have weapons at all. Look at what has happened even in modern times with piracy and civilians trying to arm themselves... almost always disaster for the civilian, and objection by governments to private military hardware not under contract to them.
And while we have differentiated the destroyer and the transport for game purposes, we don't see any difference in the series. It's a hull type that the vorlons at least think is battle worthy, and a good choice to 'show the flag'.
The point was that you could definitely have other variants of the transport. There is no reason we couldn't have a infiltration/abductor ship. Give it a lower hull, and maybe trade AA for stealth. It wouldn't have all the 'vorlon fixin's' but it would serve a role that to some degree we know was played. It would be the ship used to snatch up Jack.
So you could end up with a Patrol level ship, hull 4, 8 to 12 damage, 2 AD beam precise range 10 to 12, stealth 5+, atmospheric. The point here is a standard Vorlon ship may have a set package (hull 5, AA, beam precise) but that doesn't mean every ship they produce would be the same. They would have different tools for different jobs, you don't do surgery with a wrench, no matter how advanced the wrench.
You could do a 'fighter tender' or baby sitter ship... give it the unique trait so you don't see more than one a game. No in show basis, but as sensible as most, give a just carrier and some defenses so it could carry fighters inside closer to the fight before deployment.
It's all slightly off off topic... the transport serves a role and can be devastating. No individual transport is terribly reliable, but taken as a group you can manage some reliable damage and more importantly crit expectation.
Ripple