1 is mostly things that the publication team is asking authors to fix by email for modern journals. Most journals will have a template for these emails, or stick them at the back of the reviewer requests.

2 Is something that I have seen caught in peer review twice, and missed once. Again, it would usually go in a batch email to the authors of issues that need to be fixed before publication.

3 is definitely something that reviewers should be catching. I don't know of any journals (especially not open access) that check references for existence. Is the problem the use of footnotes? If so, I could see this legitimately requiring some manual labor / typesetting... But most journals forbid footnotes in their submission guidelines.

4 is quite rare in research articles, and again, would be handled by requesting the authors deal with it.

5. Would be grounds for paper rejection, as it breaks the submission guidelines for most journals. In addition, it seems like an exceptionally rare case.

Overall, I don't think one can justify an average of 10 hours per paper in manual labor (open access fees are always more than 1000 usd) based on these formatting issues...which issues are mostly handled by requesting fixes from the authors.

Then again, maybe your wife worked in the 1 percent of journals which actually print on paper, and carefully proofread for authors.

My background is mostly in medical engineering with journals up to IF10, though.