Modifying settings isn't going to happen. The solution, again, is to disable automatic cleaning and only run it manually. Future versions won't even allow automatic cleaning.
The proposed solution only accounts for a book saved with Sigil being opened again with Sigil and not having opened anything else in the mean time. Say you save a file and the pretty print settings are disabled and you get a warning about it. Then a few days later you need to make a tweak to another book. You open Sigil get yet another warning and choose to reenable pretty print. Then a few days after that you open the file you had saved. Your setting are back to pretty print and you run into this issue.
The second and larger issues is the proposed solution doesn't take into account books that are produced outside of Sigil that are invalid. Those files will be cleaned based on your settings and you are in the same situation. Sigil has happily "fixed" these files.
The automatic cleaning has issues. You've only noticed the issue because saving and reopening your own content has made it easier to see.