Yes, root's shell should be one provided by the distribution's base install.

I think the biggest worry is that if you need to do something like boot into single user mode for an emergency recovery, and /usr or /usr/local (with root's shell in it) is on a different or unmountable partition then you will not be able to do anything.

Say there's a failure that forces you to bail into an emergency session where you can't mount /usr/local (which is where bash is typically installed on FreeBSD). All of a sudden, you don't have a shell.

This is a really bad place to be.