Here’s what I think are the pertinent points:
These commands all send a chain length destination in millimeters to Motion:singleAxisMove() which accounts for the current position and calculates the step distance to move per PID loop (stepSizeMM) and the number of loops the movement should take (finalNumberOfSteps). Then it loops, commanding the axis is to move a step distance each time through, until the calculated number of steps have completed.
Axis uses _mmPerRotation to calculate movement from encoder changes, and _mmPerRotation comes from the pitch defined by sysSettings.distPerRotLeftChainTolerance or sysSettings.distPerRotRightChainTolerance, which come from GC $40 and $41 and/or groundcontrol.ini distperrotleftchaintolerance and distperrotrightchaintolerance.
main.py:computeSettings() calculates those distPerRotXXXXChainTolerance values from chain tolerance, chain pitch and gear teeth for each side.