The HoneyComb is at PCIe 3.0. Sadly it's at ARMv8.0 (w/ Cortex-A72) so that removes it from consideration totally for me.

And the Xavier has an official-but-still-beta EDK2 firmware available too, which includes ACPI support and can even boot Windows. (https://developer.nvidia.com/embedded/downloads#?search=UEFI...)

Yes, GPU 3D acceleration is currently not supported there yet, but the LX2K doesn't have a GPU at all anyway...