Eaves actually talks about having big (armored?) balls for other bridges, too, including those that look merely like protruding domes to the outside. There's something about that in the Malachowski booklet IIRC.
About half of his ships are called Shenzhou or Discovery studies, the other half are explicit background junk. Curiously, the highly detailed and much-procrastinated Malachowski is a dedicated background ship, when many of the others went through minimal design iterations and it was merely a matter of choosing from half a dozen slightly different but already completed doodles.
Also, many ships are called "experimental". I can see where Eaves is coming from: he has been specifically told to do flat and boxy and whatnot, and muses that the one thing he can do is experiment with nacelle placement - so why not argue that the ships are experiments on nacelle placement in-universe, too? This might also rationalize, in-universe, the spree of naming them after test pilots.
The booklets probably don't have the full dirt, though. Eaves apparently was asked to do a fightercarrier, and his Hoover was it, with the big forward-facing doors. But he also has the big doors on the Engle, and nothing about the carrier request is discussed in that context. Were there really going to be fighters buzzing about at the Binaries, perhaps dueling with the Klingon dragonfly raiders? We hear of no Eaves fighter sketches.
Timo Saloniemi