Solution: Use G92 instead of G29.1 for Z offset on A1
After a lot of trial and error, I found that G29.1 commands get ignored/overwritten by G29.4 at the end of the Machine Start G-code.
The fix: Add this line AFTER G29.4 at the very end of your Machine Start G-code:
G92 Z-0.08
Adjust the value to your needs (negative = nozzle moves higher). This redefines the Z position after all calibration is complete so it actually sticks.