I put some tape on either motor coupler and ran Y homing from different start positions, very slowly and absolutely confirmed this working in action. I've now squared the CNC, by adjusting one of the sensors until my dial gauge read the same from one end of the linear rail to the other, when sliding it along a square. It's probably not perfect, but it should do for now, at least as proof to myself that I can do it this way.
Notably, I also had to up my idle motor currents a little so it wouldn't go back out of square when they timed out. That's the I value on M906, where you set your motor amps.