When I edit a manuscript, I normally turn off Track Changes when I do HTML-coding and formatting, and clean up the author's junk that is not related to content. I do this as a favor of sorts to make the author's review easier.
Those days are over. The manuscript I'm working on never should have been accepted in its current form, which is filled with more violations of submission guidelines than almost any I've seen.
Track Changes has been on from the moment I started this project and will never be turned off.
I'm going to fill this author's (and any of his kind in the future) world with every single change I make. His right margins will runneth over with the evidence of how much I had to do to bring his work to publication.