FWIW, The Prime X299 is a slightly older version of the Intel TB3 chipset: DSL6540 vs JHL6540, though I don't believe it makes much difference, just that the Asus one isn't lead-free and has been discontinued by Intel.
The main issue with the Thunderbolt EX was that 1) it has only one port and 2) as I mentioned earlier, I can't boot with my TB3 gears plugged into it. The BIOS gives me error about too high power draw.
Well, I did do it, I posted it earlier... It has all the features the SSDT-X2990-iMacPro.aml you had (not including the TB3 hotplug)... So I've done my part of the deal
I don't believe it's going to make a difference though, as even with the exact same TB3 settings you had, the PCI list never shows any TB3 devices like your screen captures show. I believe there's something fundamentally not working here.
Even on Windows, when I boot with my Samsung S9 plugged into the USB-C port, it doesn't work. I must disconnect/reconnect the phone for it to be seen.
Without hotplug on mac, that makes the USB-C ports unusable.
The ASRock Fatal1ty X299 Gaming XE looks very nice: 10Gbit/s ethernet, two USB-C ports, support for dual-TB3 ports. And upgraded VRM ...
All the Asus doesn't have