It seems the global? setting in Preferences/Files/Saving files is ignored in favour of the same settings in Project Properties/Files/Saving files.
That is the correct and intended operation, project settings are supposed to __override__ global ones. It would be extremely confusing if one setting behaved differently to the others so I do not think this should be applied.
There is/was an issue (don't think it got to a PR) about making that fact more obvious in the UI, but I can't find it now.