One nitpick: changing registration and playing on different manuals was not common in Bach's time; some scholars have gone as far as saying it was not done, even some pieces contain explicit instructions. But it's more of a Romance thing.

Many keyboard players will play stacked keyboards today - I've got a big Nord plus a bunch of little Reface keyboards, and they often each have their own pedals attached to control sustain, rotary speaker, etc. This is basically the same situation as what you're describing (except I'm not playing notes with my feet).