Don't double check for flags in the manifest

With the recent support for r/w flags in xml files we started checking
for flags in the manfiest twice since we already had code specifically
handling flags in the manifest. This disables the new code when it is
the manifest.

Test: Automation
Flag: EXEMPT bugfix
Bug: 396992602
Change-Id: I55c1358ab38c8f35dd7ede77488feff5ad080d76