The Vasudans get all the best ships!

Since you don't know what the cylinder is for, and you don't know where to put your fighterbay, why not do the obvious and declare the rotate-y thing some kind of super Vasudan launching technology? They usually launch through those tube things anyway... so this would be practical on a ship of this size... or ... something.

It's unlikely it's anything else like a missile launcher, since Vasudans never seemed to be into that sort of thing.
The ventral beam is such a Vasudan-y thing. AAAfs on the tips of the head antenna! You know it makes sense!

N00bish: can you give us an idea of scale? I imagine it's in the 2km+ zone, but how much larger than typical destroyers is it?