In my KiCAD, the little “Preview” box scales itself as you adjust the pad properties. (I believe the nightly builds, as well as the forthcoming V6, continue this behavior ) This could give the illusion that pad size and hole size are somehow coupled, but in fact they are quite independent.
To convince yourself of this, find some part with several through-hole pads, and plunk it down on a board. (A multi-pin header strip, or a thru-hole IC socket will do just fine.) Then edit several of the pads. Make one pad larger, and another smaller. Change the size of the holes. (And don’t be wimpy about your changes - change a hole to, say, half of its original size. Make a pad 40% or 50% larger. Ignore what you see happening in the preview window.)
Be sure to close out the pad-editting dialog, then use the Ruler tool to measure the sizes of the features you changed. The Ruler should confirm that the sizes comply with the entered values, not the appearance in the preview window. (That’s an interesting characteristic of computers. They do exactly what you tell them to do -which may be, but often is not, what you want them to do.)