There's another aspect to the FJ designs that was raised in Trek Tech about a year ago (though I felt like I read it last month, because the years begin coming, and do not cease from coming) that the Star Fleet Technical Manual was as much a guide to crafting and fan-art as it was a work of technically-oriented science fiction, so the fact that the unseen ships of Starfleet could be easily built out of the pieces of an Enterprise model kit had a practical element to it, as well as a philosophical one.
As far as the ship designs go, let's remember that FJ's Tech Manual was supposed to be somewhat "interactive". That's why the uniform patterns were in there, so fans who are into that (like his daughter) could make their own uniforms, and the communicator circuitry was a real walkie-talkie schematic for those into electronics, and so, likewise the ships were mostly easy kit bashes of the AMT model for the same reason.