Despite the fact that the fleet boats had four diesels, and the Type XXI had two, I'm not at all convinced that the "fleet boat machinery arrangement took much more space than the German arrangement." The difference looks to be about 5 meters or so. That said, the reason the comparison isn't fair is that the fleet boat was optimized for long range cruising on the surface, which allowed the boat to be bigger and longer compared to the Type XXI. The fact that the Americans used conventional torpedo rooms fore and aft provided for many additional berths (29), and that freed up space for a separate crew mess, and bunks for all or almost all of the crew. The Type XXI did not have that luxury. But as I said, I believe the Type XXI offered very impressive crew comfort for its era, and was probably only second to the fleet boats in that regard.

The book you mention has little to say on the subject of submarine habitability, and what it does mention concerns postwar designs, specifically the Porpoise. An interesting book is "The T-Class Submarine," which makes clear that those boats were nowhere near as comfortable as a fleet boat. Doesn't seem close to a Type XXI for that matter.