Comment 13 for bug 1740633

Saying this is not a bug leaves a bit of a bad taste. It sounds awfully similar to the unliked "Its not a bug. Its a feature" sentiment.

You might be justified in stating this has low priority as there are workarounds in place. Or alternatively declare it as wishlist but then you need to somehow communicate to users that pad stacks are intentionally unsupported. (At least in combination with thermal connection for zones.) This might then need a DRC check to be honest.

Overlapping pads are done for many reasons not just to get arbitrary shapes. The most common one is to get thermal vias into the exposed pad of an IC package. (There you typically have one large pad with many small tht pads. The tht pads replace vias in such a case. See any footprint ending with _ThermalVias in the official lib.)
Using real vias would only be an option if kicad supports adding vias inside of footprints. (The placement of such thermal vias is critical. Especially when combined with solder paste stencil design to avoid solder wicking.)