I can't see how the system or engine would know that it's being used on 3 rail or 2 rail. I use my same DCS system on both 2 and 3 rail and different scales.
That said, there's usually some unknown quirks that aren't always obvious.
I kept an old MRC DCC system just to test stuff with before I upgrade them. Come to think of it, I never tried it with 3 rail.