In draw.c's DrawEverything, look for the two lines like this:
r_search (PCB->Data->via_tree, drawn_area, NULL, pin_callback,
NULL);
(one has pin_callback, one has hole_callback)
You want to skip those on your insulator layers.
You can skip the pin_tree ones too if you need to.
This is also the place to do "magic" specific to your board, like
drawing vias with bigger copper, copying smt pads, etc.
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