Does the controller in question handle master and slave drives on a single axis? Can it use a homing switch on each of these with defined offsets to allow the gantry to be re-squared each time you home it? That seems like a better approach which allows for the possibility that the perpendicularity is not built-in when you have a moving gantry with separately-driven ends. I agree that the ideal, and certainly in the case of milling machines rather than routers you would expect X and Y axes (and Z, of course) to be built perpendicular.

I'm following this discussion because I'm interested in where these cheap dedicated controllers are going. At the moment I'm happy with Mach3/PC/motion controller but I can see a day when a standalone box might be the way to go.