To what degree is it not square?
If you're under .5mm of X/Y distance, you'll be looking for something you think it insignificant or really small value changes in the configuration. I've seen .2-.3 mm differences clear up with a brand new nozzle (and come back the first time I run it into the bed...lol).
The auto calibration can account for many slightly off values that are not the squareness of the frame (and really you're not going to try to physically adjust for 1% tower placements for example). There's also movement based mechanical issues so belt tightness, carriage movement, arm joints can also play havok with this too. Static mechanical issues such as the arms themselves being as close to the exact same length as possible is important, if you have different lengths within a pair you'll add twist to the effector, which you don't have calibration adjustments for, but if you have them exactly the same within pairs and different between the towers you can compensate for this software wise as well.
