P.S. Average STEM paper takes about 30 hours to "produce".
Which is not to say, societies don't benefit from the system -- they actually get a lot of $$ from it. The sad part is, they only get a small part from the much bigger $$$ going to publishers.
The bottom line is: if what technies claim publishing is could be was the case then the EIC/Societies would be publishing journals themselves.
Publishers are the AWS/GC/Azures of the world. They get to collect money from those that publish papers and need papers because they provide service that the paper writers can't seem to figure out how to do themselves ( it is not very surprising - quite a few of even the well known authors of well known papers even today insist on proofs being sent to them via fax, correct those with a pen and fax back corrections ).
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.