My 2cents on the issue...
I think David's analysis is pretty much reasonable, and certainly reflects the original design intent (which, since it's written, plain as day, in MJ's own handwriting, is pretty much indisputable).
Unfortunately, we've had post-TOS shows where the folks making the calls didn't really pay a whole lot of attention to the whys and wherefores of the original concept. This was most egregiously seen when the whole "Constitution-class renumbering" thing happened, but that's by no means the only example we've got.
Ultimately, if we want to match what MJ intended to what came along in later series, we have to make decisions about what part to keep and what part to throw away...
...OR....
We can assume that Starfleet, and the Federation, are very much like their modern equivalents here on Earth... and are bureaucratic nightmares where egos and nonsensical decisions abound and trump "reason" regularly.
So...
Perhaps during the early days of the Federation, up to (and through) the construction of the Constitution-class, this scheme was in place. But the scheme got "improved" by some folks who really didn't know anything about, nor care to know anything about, why things were done as they originally were.
Maybe Fleet Admiral Hihachiro Nogura didn't personally like the "first characters are for design, second characters for sequence" and he directed that to be abandoned, instead going with a sequential system (starting just after the highest number yet constructed at the time)?
Maybe the Federation Counsel's Budget Committee found the system too confusing and pushed for a "simpler to read on this year's budget" version?
Lots of possibilities... very few which make LOGICAL sense, but plenty which would make "real-world" sense. That sort of thing happens in our world every day... and there's something almost comforting to know that the people in Trek's future really are as flawed, stupid, and ego-driven as people in our own time.
