Marked as fixed in the next release. Only admin permissions will be set by the installer (all Yes), since most admins I've dealt with don't want their users to access the wiki until they've set everything up and pre-filled some content.
I also made it so the Yes to All option will Never set an HTML-related permission to Yes. The admin must specifically choose to allow HTML. This should prevent admins from accidentally opening security holes on their sites if they click Yes to All and don't read the permissions that were just turned on.