I'm not hardcore on auto-formatters, but I think their impact on code history is negligible in the case of every legacy system I've worked on. The code history just isn't there. These aren't projects that used git until recently (if at all). Before that they used something else, but when they transitioned they didn't preserve the history. And that's if they used any version control system. I've tried to help teams whose idea of version control was emailing someone (they termed them "QA/CM") to make a read-only backup of the source directory every few months (usually at a critical review period in the project, so a lot of code was changed between these snapshots).
That said, sure, skip them if you're worried about the history getting messed up or use them more selectively.
That said, sure, skip them if you're worried about the history getting messed up or use them more selectively.