How does my MK3s even out the two z steppers?  

RE:

I'm not sure of the command, but if you do bed leveling the Z axes go full up to the stops to level themselves mechanically.  The Z motors are not controlled independently, so the Full Up procedure is needed to level the X gantry.   This is a good idea if the printer has been off for some time or if it has been moved or disturbed.

Any minor deviations are corrected for in reference to  the mesh bed leveling done before each print.  You might notice that during a print with a lot of X or Y travel, the Z axis will rise and fall to follow the contour of the bed.  If the X gantry is slightly non-parallel to the bed, this is corrected for and if the mesh leveling detects a gross error, a Full Up re-level is called for.

I suppose if one wanted to tweak the X gantry level, one would either adjust the upper stops by filing the low one a bit or by causing the bed to become higher on one side or the other.