That’s decidedly odd. Out of curiosity, when you say that that the Z-height is different, is this from a visual observation or do the actual numbers on the screen change?
One of the big problems with the Snapmaker design for CNC work is that there is a fair bit of vertical slop which gets worse the further you are from the center (on the front/back axis). Also are you homing to the center or the corner of your work piece? If it’s a visual check and you home to the corner (closer to the edge) this may be the issue.
When the motor moves the plate there’s going to be a variation in the height at the ends (think of weight transfer when you accelerate or decelerate) which is exacerbated by the use of the CNC bit which is actually driving through the material where 3D prints encounter no resistance which keeps the variance to a minimum.
There are some solutions that may help by adding a set of linear rails to force the bed to remain perfectly level at all times. Some useful threads and links: