Nothing prevents you from using 3rd party Thunderbolt enclosures with an Nvidia card other than the fact that Nvidia hasn't released any drivers. Once again, Apple has never released Nvidia web drivers, it's all on Nvidia.
Since none of the current Macs have any Nvidia GPUs, why would Apple develop drivers for someone else's products. No company on earth would offer free support for another company's products. Microsoft doesn't write Nvidia drivers for Windows either. If you sell video cards, you are responsible for the drivers for your video cards.
Maybe we should petition Apple to write drivers for Intel Wi-Fi too...