The joycon is basically a 'simper' FB-- it looks for a certain resistance(each button has it's own resistance that is connected to it), and tells the computer when it sees it, and the software defines what happens on the computer when that button is pressed.
If you are looking at using a external physical knob as well, then you might run into problems-- ie. You will end up having to set 2 different volume knobs.
It might be better to try to see if a qube/fusion brain will work better for you-- because I believe that either should allow you to have 2 software volume controls that will not affect each other the same as a software and physical knob arrangement.(though I have no experience with either product, so you should check that it will work before buying one on my advice)