Not as far as I can tell. Of course, using external controllers has some effect that depends on what you attach the controller to.I wouldn't think it would but....... will the FC's have any impact on the III's CPU?
I was editing a simple patch on the II with two different amps, two different cabs, custom IRs, a drive pedal, compression, and some reverb and delay and it told me there wasn't enough space to do any more editing unless I deactivated some things.