To answer some of the basic points (that haven't already been covered
), Gene Roddenberry was only responsible one specific "rule" which is that there couldn't be an odd number of nacelles. They had to be even to make a balanced warp field, and he seemed to think that having one nacelle was like building a helicopter with only one big rotor, and without the means to counter the rotor's torque so it could fly. Since he wasn't an actual engineer and we've seen designs that either break this rule or ignore other elements, I just ignore it myself. Andrew Probert came up with the rule about nacelles ideally having LoS between them, as with the warbird.
As far as scaling goes, I think FASA made a decent attempt of having a basic hull planform scaled to different configurations, and one can assume that each variant had the proper equipment. The Romulans created the original scout version, in keeping with the TSFS draft initially having a Romulan ship with a cloak, and they gave some hulls to the Klingons as part of an alliance. The Klingons liked the design and decided to produce their own variants, which they weren't supposed to do, as cruiser and frigate type hulls. The Romulans were not pleased when they found out and retaliated by copying the larger frigate variant and producing it for their own fleet.