Don't remove permission when cleaning up orphaned tree on uninstall

This is fixing a security bug in a relatively safe way. Fundamentally
this situation shouldn't be happening. It's an artifact of the way that
the manifest parsing is loose with types. We can consider a more
thorough and upstream fix for upcoming OS releases, but for impact risk
mitigation this is a relatively constrained change.

Bug: 225880325
Test: Tests are included for the more thorough fix.
Change-Id: I86801109ce2d9c2750c6dfef4bb0425df0ab135e