Got the page proofs for my essay in Tolkien Studies a few days ago. It took me a bit to figure out how to mark up a pdf (apparently you use Adobe -- I feel like a grown-up!) but, as I got going, I got the lurking suspicion that I'm going to irritate someone at the publishers. Only minor revisions are advisable at the page proofs stage; really, you're supposed to look only for typos. I did find two legitimate typos, and I also cleaned up a few passages where the proofreader disapproved of my original syntax but had made the corrected version much clumsier. I also fixed a number of references -- my original manuscript used the Houghton Mifflin paperback edition of The Silmarillion (second edition), having not realized that the pagination differs from the hardcover edition. The TS editors (bless 'em!) made most of those corrections, but a few of the more obscure references had been missed. So I borrowed a hardcover edition from the library and fixed that.
But that's only a bit over half the changes. For the rest, I slightly modified the wordings of a number of sentences. That's what I suspect may annoy the guy at the publisher responsible for doing the changes. Still, I try to console myself with the knowledge that Tolkien did that sort of thing all the time -- actually, he couldn't help himself, although he always remained conscious of the extra work he was adding to those poor publishers.