Add tests which cover `--apply`

We are missing tests here which cover `upgrade --apply` and hence the reboot flow we initiate which would have caught https://github.com/bootc-dev/bootc/issues/1416

To fix this in the tmt tests we probably need to add `tmt-reboot-prepare`; actually I filed https://github.com/teemtee/tmt/issues/3886

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That said we can and should cover this with a testing flow that runs outside of tmt; actually I'd like to have some of our tests create machines which don't run ssh at all and report their status instead of being puppeted over ssh. Something like an "e2e-upgrade" test that runs a complete scenario instead of being synthetic too, i.e. run a representative workload.

Of course more ideally tmt would support something like that, but it'd be a pretty fundamental change for it AFAIK.