>the presubmit can stack the changes into two commits
That seems like way more complexity than just doing it once and for all. Now the commit log is littered by a bunch of automatic commits that format one file at a time.
The commit history for untouched files is mostly just cleanup CLs for reformatting or changing an import for a decade+. A lot of the history is rather useless for finding a bug but at least its generally well tagged with 'CLEANUP=TRUE' so you know to ignore them.
That seems like way more complexity than just doing it once and for all. Now the commit log is littered by a bunch of automatic commits that format one file at a time.