> I don't actually write much Python, but surely you could have run the same tool (or some other formatter configured to match the linter) locally to have it do that auto-format for you?

Maybe... I don't work there anymore, but if I'm ever in a similar situation, I will consider that approach, assuming it will only reformat files as needed. (I suspect the company-mandated flake8 script scanned all the code (200K lines), rather than just the files that changed, considering how slow it was.)