Humph, got myself stuck with this same issue…no way to specify a pad for a single layer anymore in KiCAD 6.0…
In my case, I have a screw connecting to the B.Cu layer, and obviously going through the board. A high-current power plane on the F.Cu layer goes around this screw hole–but does not need a 10mm gap (as there’s an insulator on the top of the board).
In KiCAD 5.x.x, setting the pad to “B.Cu only” would only apply the “hole clearance” on “F.Cu”, leaving a neat little clearance around the hole. In the meantime, the “B.Cu” would have the pad + the clearance, of a significantly larger circumference.
In KiCAD 6.x.x, I can’t set “B.Cu only”, and now the “F.Cu” layer gets a needlessly huge 9mm clearance around the hole–because of the “B.Cu” pad diameter + clearance. This huge gap reduces the amount of copper available for current carrying on the “F.Cu” layer.
Guess I have to edit the kicad_mod file by hand to get the previous functionality back…because KiCAD 6.0 can easily display it, just as soon as you edit the pad, it all goes wrong due to the missing setting…
KiCAD 6.0 with the B.Cu pad clearance applied to the F.Cu hole clearance.
KiCAD 5.x.x with the separate clearance applied to just the F.Cu hole:
(also notice that the “mask” layer has an opening for the hole, unlike KiCAD 6.0)
Bit of an annoyance, that’s for sure. Special case, I suppose…but sometimes we move backwards.