Of course they were "manipulations". To quote the man himself, "the negative is the score; the print is the performance." During the course of a long career, Adams' opinions about how his prints should look changed. Any of us might discover this; if I was to go and reprint a neg from 25+ years ago it's likely I'd print it differently. A key difference in this is, of course, that Adams had (I should say made) a market for his older images, unlike myself...
Remember also that the Zone system is not about the literal transcription of light values- but being able to control them to achieve an emotional result. Which Adams did.