Special:ManageWiki/permissions/user needs a "reset defaults" button for each section. (Or call it Restore defaults.)
After clicking it only the original default boxes should become checked, just like they were on day 1.
The user could then hit the submit button if he is happy with the selections.
It should be clear that hitting "reset (or restore) defaults" only changes what he sees, not other sections of the form.
Reason: it is easy for users to mess up their wiki and then have no reference as to what the original working settings were.
In fact perhaps each section of each ManageWiki page needs a "restore defaults" button.