I did a little video to talk through the scenario and some possible solutions to a non-square gantry movement. Here it is:
Let me know if there are any parts that are unclear, but in a nut shell, it doesn’t matter so much that the frame is square as long as the spindle movement (X to Y) is square, so to get them square you may need to take the frame slightly out of square, and that’s okay.
I’m sure it’s not Ideal, but okay if it gets the cuts perfect, and eliminate the extra step of blocking every power up, right?