PackageManager: Let system-defined permissions take precedence over settings

If a permission was already present in the device's settings due to having
no prior system definition, and the system tried to take it over
(after a version upgrade, for example), it'd fail, since the saved
value would clobber the one previously read from the permissions XML.

This breaks system-behavior changes (gid grants, in particular) unless
the user performs a factory reset after upgrading, which isn't acceptable.