I use a CSMIO/IP-M to run a two-motor X axis (i.e. X master with A slaved to it). The controller "supports" this mode only as far as copying X output to the A output, in effect just ensuring that it keeps the two axes in sync. There is no dual-homing mechanism (you have to pay around 3 times as much for the IP-S for that, although it does do the job very well). To make sure that the gantry is square, at the beginning of a session I home the axes in the usual way. I then hit e-stop, which takes power off the steppers and I can turn the A stepper by hand. Both X and A axes are fitted with home switches. The X axis home switch is used for normal homing but by turning the A motor, I can adjust until the LED on the A proximity switch starts to flicker. I have adjusted the home switches and their triggers so that the gantry is square when both X and A just trigger their respective switches. So, I have now manually checked that the gantry is square (to within a step or so on the motor, which with 5mm lead ballscrews and a metre-long gantry is pretty close). I can reset the control box, do another homing operation (both because Mach3 insists on this after a reset and also to double-check that all is properly homed) and I'm ready for machining. It is very unusual for the gantry to go out of square unless I hit e-stop during operation or I get a motor stall (rare now that I have tuned things). Even between sessions with everything shut down and restarted, the gantry is seldom out of square by more than some tiny amount.

You might be able to do something similar with the controller under discussion as the squaring adjustment is completely independent of the controller. I keep thinking of trying to automate the "manual" steps here, but it's so easy to do it's hardly worth the effort.