As far as the Fire arcs...I'm going to have to tinker with it when I get the model in the Vision engine, but more than likely it will have a poor fire arc anyways just based on where the turrets are

...Which adds to a difficulty level when facing the bugs
The Bug Transports suffered this same flaw in WCP/SO. Their bow turrets - and their Aft turret too, now that I think about it, are both mounted on the topside of the ship, meaning an attack on their belly would avoid the fire. (Though in retrospect it's not really possible to hit the Engine with a torp if you're attacking the belly of the beast).
Another good example of this is the Star Destroyers in XVT/XWA. They have most of their weapons placed on the topside of the hull, making it possible to eliminate the turrets on one side of the ship and then constantly strafe it until it explodes. That was also somewhat irksome to me, as I had little difficulty stripping capital ships of their weapons, and then disabling them so they couldn't escape while I destroyed them.
I'm not sure if it's possible, but it would be nice to see the AI concentrate attacks from the bottom of the ship if the firing arc is so limited. You might not be able to script that into the AI, but you could always make sure the enemy ships spawn at a point below the plane of the transport, so they would be "Rising up" towards it as they engaged.
A relatively simple roll would do wonders to counter that tactic. Maybe we'll see some of that in your mod!