How about treating it the way certain antenna patterns are treated. Make your footprint out of copper and put two pads on the same net. I know this is easy to do but don't recall how. Sorry.
There will still be an unsatisfied ratsnest connection between these pads that DRC will complain about. It wants you to connect both of those pads to the net with actual traces -- avoiding which is exactly the goal of creating wire jumper/link footprints. KiCad does not treat pads with the same number as "internally connected", nor there is a way to assign multiple pads to the same pin.
There is an EIGHT YEARS OLD issue in the KiCad issue tracker: https://gitlab.com/kicad/code/kicad/-/issues/2004
Implementing this is obviously trivial:
if (pad[a].pin_number == pad[b].pin_number) {
mark_connected(pad[a], pad[b]);
}
, so I believe there is some strong opposition among the developers, which I cannot explain, to this very basic feature that has at least two very obvious real-life use cases, whereas I can barely imagine any use case that would be broken by treating pins with the same numbers as connected.