Fix the isSystemApp flag for APEX

Re-land ag/17321991 with tests fixed.

To be consistent with the behavior of system APKs. An updated
APEX (in /data) is still considered as a system app.

Fix tests by checking the FLAG_UPDATED_SYSTEM_APP flag instead
against updated APEX.

Bug: 225760014
Bug: 225756739
Test: atest CtsStagedInstallHostTestCases \
            com.android.server.pm.ApexManagerTest \
	    GtsStagedInstallHostTestCases \
	    StagedInstallInternalTest \
	    com.android.server.pm.parsing.PackageParserLegacyCoreTest
Change-Id: I4d59cc37ca388ba3c8d22c679b17ede6720d1d03