freebsd-update: create deep BEs by default

The -r flag to bectl needs to go away, and we need to just do the right
thing. In the meantime, we can apply an -r in freebsd-update as a
minimal fix to stop creating partial backups in these (non-default) deep
BE setups.

PR: 267535
Approved by: re (gjb)

(cherry picked from commit 989c5f6da99081b1f2b76ec09e91078e531e1250)
(cherry picked from commit 5c2a559876d123ba386612319bf42e7b32dee590)