Yea… Seems a bit of a poor design choice to require homing and squaring be coupled, when squaring relies on accurate limit sensing, and the OEM switches are just not accurate.
See:
Personally I’ve de-coupled these two, and only square up the machine when I am certain the switches are clean. Normally, if I don’t suspect something is out of whack, I just run homing with a single switch that closes both L and R circuits.