"Starship' was a term for the deep space vessels, the ones with the longest range and that would be away from "home" the longest. So you could have the cruiser be a starship, or a heavy cruiser, or even a scout of a different design-- but probably not something like a destroyer-- too short range by design. FJs best skills were in flushing out the unseen areas on the ship-- making all the crew cabins fit in a logical way was amazing. Plus there's no logical way to have a round corridor in the secondary hull. No point to having a corridor follow the outside circular shape of the hull, just to get a circular corridor down there-- the windows tell us that much. Also, hard to believe the Enterprise and others like her were the best of the best because they were already in service for awhile. I would think it'd be more believable to say they were the best when they were built, like any ship is, but they've been away on their missions so long that newer ships have probably been built. Also why things looked so different in the universe of TMP-- once the Enterprise made it back home, the only one, the tech had advanced while they were gone.
I bet anyone who recreates the FJ plans will end up with more of what he did than they even think-- his layout just makes that much sense in most areas!