Manual (3DP) bed calibration on home-made quick-swap arrangement

I am having an issue with the subject above:
Everything is as standard (single extrusion) except that the print bed and heater bed are higher than normal by about 24mm due to a home-made quick-swap arrangement on top of the original CNC wasteboard.
The automatic levelling works well (5x5) but the head does seem a bit closer than normal during the initial probe at each point.
But, when starting the manual levelling calibration, the head comes down at the extreme left location and crashes into the bed, the nozzle itself is beyond the edge of the bed at this point.
There seems to be nothing I can do to stop it descending in order to start levelling from a higher position.
Is there something I am missing here? Or is it hard-coded into the manual levelling process? Would I benefit from telling it I had the Snapmaker quick-swap kit in the settings (which I don’t of course) to start from a higher Z?

You’ll likely have to use z-axis spacers on your linear modules as well. 24mm is too extreme to compensate otherwise. Or some sort of offset adaptor in the print module itself.

That there is a small gap in the automated calibration is normal. You are not calibrating the nozzle tip.

You calibrate the hall senser. This one should light up red.
Only the last spot should be calibrated with distance card. Because single extruder has no automated endpoint.

Activating the Quick swap and bracing kit could do the trick for you (not sure if bracing kit is available yet).

Did I understand correct, automatic leveling works and manual does not?
Are you able to abort the fast z travel process by actuating the probe sensor?