deploy: Fix removing /var/.updated with separate /var mount
There's some subtlety to this, we don't handle all cases.
But the 99% cases are using `--sysroot deploy` to create an
initial deployment, and then doing upgrades from inside
a booted deployment.
It was only the latter case that didn't work with a separate `/var`.
Fixing all of them would probably require libostree to learn
how to e.g. look at `/etc/fstab` (or worse, systemd mount units?)
and handle the mounting. I don't think we want to do anything
like that right now, since there are no active drivers for the
use case.
Closes: https://github.com/ostreedev/ostree/issues/1729
Closes: #1730
Approved by: akiernan