I’d just like to note that, at least according to Probert in the interview with Trekyards, that the specific ship Gene objected to was actually the Single engine Destroyer/Scout, an example of which Probert had roughly sketched in another dry dock, near where the Enterprise was being refit. When Gene viewed the sketch (no doubt in a foul mood with FJ for reasons other have expounded upon, which if anyone is framilliar with his shenanigans with the theme song lyrics isn’t really a surprise), he told Probert that “warp drive needs two engines”, which the later took to heart. Also Probert said the 50% line of sight rule was intended to be strictly line of sight.
I think this pair rule was also a pretty common thought before hand though, both on Jeffries part and later on the part of Robert Kline. The later has stated, again to Trekyards and with many years distance so a grain of salt prehaps, that it was also his impression that two engines were needed for warp drive, and he had no real direction other than TOS for designing ships. Supposedly he was also aware of the line of sight rule. His work actually predates the Tech manual... which leads me to believe that really although Gene made it a hard rule at least for hero ships, it probably was the generally accepted fan /production crew view pre-FJ, so while he may have acted out of malice it wasn’t an entirely arbitrary decree so much as making one school of speculation cannon over another. And AFAIK Jefferies gave all his warp ships that made the screen two engines (and a top mounted bridge, and a sensor/deflector), and even the supposed impulse driven Romulan BOP has two engines.
As for the rules, in my opinion they actually should be stated as “Roddenberry’s rules; and the Probert Corrolary”, as from what Probert has said the line of sight rules from the front and side views of the ship seem more his doing than Gene’s (though I’m sure he gave the corrolary his de facto blessings by approving designs that adheared to it). To me it seem the rules should be:
Gene’s Rules:
1. Paired Engines!
2. Bridge at the Top of the Saucer!
Probert’s Corrolary:
3. Engines must retain line of sight, P-S & F-A.
Although honestly I don’t know whether it makes sense that the whole having the engines visible from the front was a rule that originated in the TMP era or the TNG era, but I can’t think of a ship from the movies that violates it... maybe the Excelsior? I think that one was more something Probert chose for visual congruity since having los in one view of the ship but not another would look funky.