I guess "it won't work" depends on what you're using it for.
A "true" thunderbolt adapter just serves as a bridge between the host system and the PCIe device. The device would show up like any other PCIe device to the host, use the same drivers, and function identically as it would if it were installed in the host machine.
Problem is, the majority of computers made do not have thunderbolt controllers. So, if you want to attach one of the high speed NVMe drives to any generic computer, you need to look like something most computers do have, and this is basically always USB. The enclosure you linked has a CPU or at the very least, some complex state machine and a PCIe root complex. It makes the PCIe connection with the NVMe disk, but it presents itself to the host computer as a USB Mass Storage device. The host has no idea what kind of physical storage is on the other side, just that it complies with the USB Mass Storage specification. You can't access anything specific about the device.
So, unless your goal is to turn the FPGA board into an NVMe device, you won't get much use out of a USB to PCIe enclosure. If you want to use Xilinx XDMA, LitePCIe, or something else, you'd need the thunderbolt to PCIe enclosure.