How to handle components that literally share a footprint?

Continuing with my OpenVPX learning, I've run into an issue with connectors that are placed on the rear side of the backplane, but use the same through holes as the usual front-side connectors. Literally, as in the connectors are press-fit into the exact same holes, with the pins approaching each other and only not colliding due to the thickness of the board.

The problem is that I don't know how to approach this when setting up symbols and footprint components in a sensible way.

On the symbol side, I could create a heterogenous part, build the two connectors, name them appropriately, and assign one "double-sided" footprint to this symbol. However, then I only get one count of the connector in the BOM when I really need two (or, a second different connector, depending on the connector series). Alternatively, I could also create two individual symbols, assign matching footprints, and place them on opposite sides of the board, overlapping all through holes. This would get me the proper count and part numbers in the BOM, but generate hundreds of DRCs that I would have to waive.

So, is there either a way to a) assign multiple, possibly different footprints to a schematic symbol and having that reflected in the BOM or b) overlap two parts as described above without generating the massive quantity of DRCs? I'm leaning towards the second option because messing with the BOM is a good way to cause problems in my experience.

Thanks!