I was just about run the program for my waste-board when I realized that I have the same issue. I can’t believe the instruction video does have you check diagonals.
Not sure I totally follow the bolt holes method as there is enough play in the holes to still allow a margin for significant error.
Mine doesn’t seem to want to square. I am wondering if my Y bars could be holding it skewed. I will try loosening it tomorrow.
I have an idea for a 3D printed three sided jig at each foot that could be used to get it into position and hold it while tightening it down.
Another idea of onefinity would be they could provide a bolt hole template printed on Mylar or plastic that could be laid out.