I don't update Linux, FreeBSD, or any other OS in place except on my FreeBSD-CURRENT desktop. The only way to operate in production is to create a new VM from your template, apply the runbook/state/whatever, route everything to the new VM, and drain the old VM.

My personal systems aren't where they should be for CM, but I still can't think of a good reason to update in place rather than rebuild and copy over configuration/data.

Flavors should make it easier to operate with packages instead of ports, but I don't have any idea what's going on there. If I were supporting a large number of systems, I'd want FreeBSD over Linux any day of the week and twice on Sundays because the ports system doesn't make you choose between a stable OS branch and current software.