Don't always filter out --auto-add-overlay

There are some cases where --auto-add-overlay is added for legitimite
reasons, for example in RROs.  Only filter it out from modules that
were using --extra-packages for support library modules.

Test: m FORCE_AAPT2=true java
Change-Id: I165fa577f2204ecbc57e71f946db3f346568ad81