"You seem to have misunderstood. The TM completely dumps the so-called Jeffries rule of starship numbering - that is the "alternate interpretation" I'm referring to. FJ's ship classes don't start out with -01, or even -00 in all cases."
So we should follow the learner (Joseph) because the master (Jefferies) didn't know what he was doing?!?
"Which is one of the better precedents the Manual set, as it bumped the pompous Paramounters down a peg or two - a position where they rightfully remain even today."
Excuse me, but the "pompous Paramounters" you are refering to are the creators of Star Trek!
The term "Enterprise Starship Class" originates from the show's producers Bob Justman and Gene Roddenberry.
I suggest you visit the thread "NCC = Not Constitution Class?" where I quoted these original "Enterprise Starship Class" statements from The Making of Star Trek.
In my latest post there I also offered a solution how to rationalize the prefixes beginning with 16, now that these have been established by TOS-R.