In the Olden Days <TM>, proofreading was done by two people: one reading aloud, and the other following on the proofs. Or so I'm told.
FWIW, I worked in book production for 16 years. No matter what the stage of production, an author was never charged for the correction of a legitimate error (e.g., a misspelled word missed by the copyeditor, odd word breaks introducted by the compositor). However, authors were always charged, including in galley proofs, for making changes that were not related to actual errors that were somebody else's fault. For instance, correcting "blu" to "blue" wouldn't be a charge. Changing "blue" to "indigo" would result in a charge. And years ago, in galleys or page proofs that charge would be something like $1.35 for the line that contained the charge and another buck or fifty cents for every line to the end of the paragraph, which is how the charges added up so fast. In pages, there would also be a remake charge. This was in the days when final product was film, so we're talking a few years, now. Things might be different now that everything is so digital. Also, this was a nonfiction environment.
On the other hand, as long as these "AAs" ('author alterations') didn't exceed 10% of the cost of composition, the publisher ate the cost and didn't apply it to author royalties. So there was some leeway, however small, for your indigos.