Have you seen the compute module though? It exposes a PCIe slot via a separate I/O board. At first I assumed there was some free lanes, but now I see it doesn't exposea usb 3.0 ports, only 2.0.
Still, I would rather have a dedicated bus for storage with usb 2.0 rather than usb 3.0
Besides, the device is $70. A $10 32GB eMMC chip would be a far more reasonable ask at this price point if greater reliability is desired.