Not sure that last bit is correct; the 17th cruiser design sketch also shows him working out design details on the secondary hull, like the clam-shell doors and the sensor dish. Also, his signature there is more consistent with the ones on the earlier ball-and-stick Enterprise sketches than the later Phase II stuff.
Well, honestly, I'm indifferent to when that first drawing was done. It may well be that this note was there from pretty early on and only MJ cared about it. But there's nothing on the drawing that indisputably proves it wasn't part of the Phase II
He was attempting to redesign (or "modernize") the ship during the Phase II
work, so it seems more likely to me that any such "modernization" notes would be associated with that project... or else Matt was just really foresighted. could be that he included a sketch of how the old ship was arranged, just to have it on his drawing board for inspirational purposes. Maybe in his designing a new version of the ship, he had hoped the clamshell doors would actually be able to slide open on the model... there's no way to know (unless you're privy to more information than I have in these books... if so, please do share) no way to know exactly what the purpose of the sketch this note is included on was for. But, the drawings of a dimensioned model of a 60" long very TMP-esque Enterprise
which also bear the "1701A" nomenclature are clearly dated "6/77" as are a few other random sketches.
As for his signature, I just thumbed through several of his sketches in the books on my shelf and the style of handwriting goes back and forth a bit, it's hard to nail down an evolution in that regard. The "6/77" drawing bears a signature very much like that on a few of his ringship drawings and we know how early those were in the pre-production sequence. I just don't think the shape of his signature is that telling in this case.
One thing we can be fairly sure of is that, if indeed the "1st MODERNIZATION" notes were on a 1964-5 era sketch, that Jefferies probably thought it was actually a pretty good idea and held on to it pretty firmly if he brought it back up 12-ish years later. (Or, he might have come across his old sketch and thought "oh yeah, that is a good idea" and wrote it on his new drawing.)
But, it seems more likely to me that all those drawings are contemporary. But, I couldn't say for sure. I guess I'm 60/40 on the matter.