The rules were never stated onscreen. Thus, despite Word of God, they are fanon.
They may not have been stated on screen, but the Model and Art Design people took them as Gospel, so they built all the Federation Ships to match those rules. Not every little thing must be stated on screen for it to be the case. It was clearly the intent of the makers of the various series and movies (at least until the JJ reboot) to follow those rules.
Actually, as far as I can tell, the 'Model and Art Design people' NEVER paid much attention to them.
The SS Aurora violated many of the rules.
The USS Saladin and Hermes showed up on technical readouts.
The USS Grissom blocked the nacelles with the saucer.
The USS Excelsior occluded the nacelles from the front.
The USS Freedom had one nacelle.
The USS Enterprise AGT had three nacelles.
Another TNG (forgot which one) had threee nacelles.
The USS Defiant blocks the nacelles from one another.
The USS Sydney blocks the nacelles from one another.
Several DS9 bashes violate most of these rules.
In fact, I can't think of any period
at all where these 'rules' were enforced. Even as early as TNG season one, the Oberth/Grissom was used heavily, as was the Excelsior... so...