When starting out with KiCad I thought the same, though much experiment revealed that there is no need to set pad size less than drill size. Equal seems to work best.
I keep solder mask clearance at 0.1 mm which propagates correctly including NPTH.
As for silk screen. The board designer must ensure pads are free of anything that does not belong into a pad! Some fab houses leave it as is (ugly results). Some mask it out (ugly results as well).
Best practise is to check meticulously against a fab’s house capabilites. Just one example.
Cheers