Prevent overridden APEX from being installed even when flattened

Previously, both overridden APEX and overriding APEX were installed
together when TARGET_FLATTEN_APEX is set to true. This was because the
Make modules for flattened APEXes are phony where
LOCAL_OVERRIDES_MODULES isn't respected.

Fixing the problem by letting apex_manifest.pb for the overriding APEX
to override all modules for the overridden APEXes.

Bug: 147384966
Test: OVERRIDE_TARGET_FLATTEN_APEX=true m dump-files | grep
mediaprovider shows

:   out/target/product/coral/system/apex/com.google.android.mediaprovider/apex_manifest.pb
:   out/target/product/coral/system/apex/com.google.android.mediaprovider/apex_pubkey
:   out/target/product/coral/system/apex/com.google.android.mediaprovider/javalib/framework-mediaprovider.jar
:   out/target/product/coral/system/apex/com.google.android.mediaprovider/lib64/libfuse.so
:   out/target/product/coral/system/apex/com.google.android.mediaprovider/priv-app/MediaProvider/MediaProviderGoogle.apk

only

Change-Id: I6dc3fc7aaee0474cbad9fadbfce765be4b751328