Move logic to disable flattening in unbundled app mode from Soong to

make.

Avoids TARGET_FLATTEN_APEX lying about it, so we can trust it in
scripts, e.g. in art/build/apex/runtests.sh.

Test: banchan com.android.art; art/build/apex/runtests.sh
Bug: 179900989
Change-Id: I5361957c448e61634689968424450420479f6111