Don't remove non-installable apex deps from the system install

We were marking any libraries included in any apex (including
non-installable apex's like com.android.runtime.host) as
uninstallable. This could cause phones to become unbootable if these
apex's are modified.

Bug: 123892969
Test: m droid && boot device.
Change-Id: Ief9004bbe7b106ee8f52715ce5bd7bb5accec290