Insulated Metal Base (IMS) PCBs are quite sensitive to shear strain on the connections, since the insulator tends to be brittle compared to FR4. Even if the static strain may be acceptable, it is a preload, so if you add vibration on top, you may well fatigue and crack the insulator around the connector's footprint pads.
It is best to use a couple of alignment pins to line up the top and bottom boards, and then use shear-less connectors, i.e. connectors that are free to move in the plane of the PCB.
Pogo pins would do this job well. I don't recommend zebra strips if longevity is desired - they are OK in limited lifespan consumer gear, but a bad idea otherwise.