Considering that in the only scene we ever saw within a Raider Carrier they had gravity, I'd say the rotating rings also contain the crew quaters and the big non-rotating sections only contain machinery and storage rooms. Being a pirate ship it would make sense to have lots of space for the bounty.
But considering how Babylon 5 starts it's fighters, I'd say the Zephyrs shouldn't start straight ahead, but rather go away from the center of the ship diagonally (momentum from the rotation plus engine power of the fighter).
And they probably have to temporarily stop the rotation to dock the fighters...
But your right, while parts of the ship make sense, overall it's a very inefficient design. Which probably fits the rag-tag feel of the raiders in the opinion of it's creators.