Wouldn't it be practical to keep all PCB layers clean under the ground paddles; use a hole punch to cut out the PCB epoxy under the chips and mount the real heatsink on the bottoms with copper washers/thermal spreaders? The tops would then just need a mechanical clamp.
Instead of cutting the PCB, place large exposed solder pads on both sides of the board, connected by lots of vias. Then just mount the heatsink to the exposed pads on the underside, while the thermal interface on the bottoms of the QFN packages get soldered to the connected pads on the top side.