OK 3DP got it. So when bed leveling is on (M420 S1) the machine will not move to negative Z coordinates. You can change that by disabling bed leveling (M420 S0).
To run an auto calibration though, and just let the machine do its thing, do this: Is automatic level compensation working properly?
Don’t use G1029P11 though, you’ll want G1029P3 for a 3x3 grid to start, or G1029P5 for 5x5. The rest is the same though.
If you follow those instructions that will also reset where Z=0 is, so the nozzle will touch the bed.