Supported PCB formats (via-in-pad related)

https://jlcpcb.com/help/article/pcb-via-covering  states that you prefer original CAD files over Gerber files in order to correctly identify which holes are vias (and should be filled+capped) and which are through-hole components (which must not be filled+capped). Which file formats do you support for that?

I tried uploading the KiCad files but it didn't detect any layer and doesn't show a board size either.

If you only support formats other than those used (or exportable) by KiCad, how should I indicate which holes should be filled and which should be left open? I noticed the Gerber viewer showed holes (gray background) for some via-in-pads and no holes (green background) for other via-in-pads even though the drill file uses the same tool (annotated with`ViaDrill`) for those holes.