The user is able to install new certificates.
That's true today, but there's no guarantee it will be true in the future. Google is already pushing for all software running on Android to be cryptographically verified and they (Google) are the only ones that control the signing keys. This means that they intend to kill off F-droid and all other software delivered outside the Google store.
If Google is able to pull it off on Android, everyone else will try to do it on desktop OSes too - Linux included.