I would recommend you use the number you measured. Chain tolerance, chain stretch along with chain sag are known limitations to the automatic motor distance calibration.
As an example, one of my chain pitch tolerance is 0,12%, which already creates almost 4mm difference. Yet chain sag prevents the chain to reach flat horizontal in the calibration execution, and chain stretch is typically around 6x10E-6m/m/N which nears 3mm over 3165mm when 40 lbs pull is applied on the chain.
I invite you to “find your X center position” to start tuning the chain tolerances and learn more about the maslowCNC nature.
Then among the Maslow community, there are several interesting improvements on their way to better automate calibration of the Maslow CNC. I invite you to browse into the forum posts. Notably the coming Holey calibration.