"If you're concerned about registry numbers, don't be. You can make them anything you want. There's no rhyme or reason to them. Whatever "Jeffries rule" may have existed, doesn't have to be binding."
Dear Sir,
I'm aware that a Grand Unified Theory, mind a TOE, for the Universe of Star Trek including all series is rather next to impossible than improbable.
However, if a theory that limits itself to observing the original series and its subsequent films (!) answers more questions than it's raising new ones, it should be applied (especially given all the changed premises in Star Trek where new people didn't understand what the old ones intended) rather than being thrown out like a baby with the bath water, in my humble opinion.
According to my understanding of canon, something is most definitely canon if it is what the original producers and production designers intended and if there's no substantial evidence to the contrary (i.e. screen or dialogue information), then it is canon. Therefore the 'Jefferies Rule' (creator of the Enterprise!) should be binding, unless you've arranged yourself with the permanent Retcon Maneuvers that plague or beloved Star Trek.
Bob