Allright, bridging the Top Pin (NC on the PCB) to the bottom one (io3.in) did the trick.
I had to invert the signal but other than that no changes were necessary on my firmware configuration.
For future reference and anyone who is trying to do something similar:
M950 J1 C"!^100.io3.in" ; Tool1 docking detection GPIO setup
Is the command I use now.