Downside of using superspeed pairs as USB 2.0
It’s pretty common to leverage the USB cable for other things. One that comes to mind is the PCIe ‘bitcoin miner’ external adapter that connects one PCIe Tx/Rx lane pair on the SS set and sends clock over DP/DM.

Anyway, based on the discussion I think that just using the standard 4 wires for USB2 and Vbus/GND, and reusing the SS pairs for your other signals is perfectly fine. There’s no benefit to using a SS pair for DP/DM and I don’t recommend it, as there is the possibility of connecting your signals to the USB2 PHY.

In planning how to use the SS pairs, note that the TX pair (inbound to the device) will have DC blocking caps on the host side, while the RX ones (outbound from the device) are connected directly to the PHY.