I've have been getting XOR differences, even after all the procedures are being followed. What exactly does XOR check in precheck does.

It checks that the connections to the caravel/caravan framework are as expected. That is, that the wiring around the outside of

user_project_wrapper

or

user_analog_project_wrapper

matches the expected wiring. You might want to look at this: https://skywater-pdk.slack.com/archives/C01E06TUSC9/p1652941742085029