Hi Paul,
I have exactly your problem. I have physical switches and several functions like BRAKES, STATIC ALT or FUEL PUMP have only the toggle option which is of course not compatible with our setup. There are also some ON/OFF options which are not working even if are selectable in the sim (eg., NAV, TAXI, BEACON lights).
The bad news is that I reported all this issues 6 months ago during the alpha testing, the support team flagged that as solved but no available fixes at the moment. I guess they have it in the backlog and actually I feel annoyed to report these small issues without any visible feedback.
Hope they could fix that at some point.