you can use midi controller and footswitches simultaneously assigning them with different commands.
Unfortunately footswitches are limited to two switches each for both devices and there is only a fraction of functions you can assign on them if you compare to the vast Midi capabilities.
you might wanna check the below video link for a little demo that i have recorded.
BB + Boomerang looping - #7 by Nepali_brother
Midi thru is implemented throughout this pedalboard.