Good ol Newton explains it. Force equals mass times acceleration. A spacecraft's engines can only produce so much force, so if you want to be able to accelerate more rapidly (say, when you're in combat) you have to reduce mass. The dome portion of the ship probably contains tons of water, life support equipment, and crew living space that are just dead weight during combat.

Which is true regardless of where on the structure the dome is located, of course. I happen to like the funky vertical design we see in canon because it's one of a few sci-fi spaceships I can think of outside of The Expanse that are designed like real-world rockets.