Pass APK_IN_APEX flag when parsing apk in apexes

Not caught in unit tests because this is more an integration failure
(detected when writing e2e tests).

Bug: 208239394

Test: the actual e2e test will be published when this is submitted
Test: m ApkInApexTest
Change-Id: I8b62e473e2b3613cf290ff05963a47ba86140d99