Hm. Normally you define drill holes as a footprint (< 6.35 mm).
If you need a special clearance for them to copper, just adjust the local clearance for those NPTHs?
For that matter, clearance to board-edge can't be set in KiCAD either..
The clearance for PTHs should be determined by the annular copper anyway.
But I get that inner layers demand a bigger clearance than the outer layers, because of layer-layer-placement tolerances.. KiCAD can't do that yet.
That's why I asked what kind of drills we're talking about here.
And using overlapping drills for slots is just really really bad practice. Drills are drills and not milling bits.
If one needs slots they should be created via milling and defined accordingly.
Overlapping drills is begging for trouble.
Any fabricator who can't mill slots or any ECAD tool that can't define milling slots (plated/unplated) should not be used anymore IMHO. We've got 2017, not 1967
And placing drills close together, again, we got the drill clearance that we can set, as well as give us some human help by drawing a circle on the x.Fab layer to define a clearance area for the drill footprint. All my NPTH footprints have that.