Update:

Tried the Marlin RCBugFix version and the same problem that I had before still prohibits me from lowering the nozzle so that I can calculate the z-probe offset.
Even if I change the Z min to -2 I couldn't lower the nozzle, so I'm basically back to square one.
I think I will get a new glass since the one I have ain't totaly flat, a few 0. mm apart from corner to corner and try that out and see if it helps.

Q: Does it matter if G90 is placed after or before G29 in the gcode?