They didn't. I don't know what he's talking about.
I have heard that the CLassic II had two different ROM configs, but I thought I read that in Pina's book. Guess not. The Apple Service manual makes reference to it that the logic board can have two or four ROMs, and that they are otherwise identical. It also identifies the different logic boards as the same part number. Apple's own Developer Manual specifically lists the 4 ROM chips (see pg. 13).
Aside from manufacture date, were your Classics built in two different locations? There could be some localized reason for the logicboard change by manufacturer. Obviously the two chip ROM and the speaker perforations are in the later Classic II, which obviously coincides with some update in the design. Pina does reference the speaker addition where he provides the perforation template for retrofitting a Classic with the holes. So likely it all occurred at the same time. CORRECTION: Just looked at the Pina book, which is copyrighted 1993. Since your Classic II has a manufacture date of 1992, and Pina's book only mentions the 4 ROM chipped logic board, but also the speaker perforations, the case modification happened before the logic board change, or Pina did not think it significant enough to comment on. I find the SE/Classic book on the whole lacking quite a bit more detail than the original Plus book. So the Classic II came out in late '91. The released as the Performa 200 in September 1992, so that's probably when the speaker grille appeared. The logicboard may have changed then too and Pina simply did not discover it in time to revise the book (not having opened one), though the case perforations would have been pretty obvious. Or it appeared even later in the year.