In case anyone has a similar need, I found a way to gracefully shutdown Bela through a MIDI command in Pure Data using the [Shell] external from this repository: https://github.com/reduzent/pd-ggee/blob/master/control/shell.c
Sending it the message "halt" opens a terminal shell and executes the halt command.
I wired it to respond to a MIDI note so that I don't need a dedicated shutdown button on my enclosure, which is ideal for my use-case (stashing it under the pedalboard).