By now there are many SSDTs for Thunderbolt, almost all of them seem to work, in fact the key to the hotplug seems to be the "PCI-Thunderbolt One" _DSM method on PXSX.
So I don't know among all the rest what the most correct values are.
What I noticed in my new Gigabyte X299 build, is that the THB_C connector prevents MacOS from detecting the thunderbolt card if no device is connected.
If I disconnect this cable, the Thunderbolt card is detected even without any device connected at startup, but the hotplug seems not to work properly.
Currently I have the card installed in slot 4 and the THB_C cable connected, but to work and have the hotplug, I have to have a thunderbolt device connected at startup, in fact I have a THB Dock that turns on when the computer starts, fortunately.
I think the problem of not recognizing the card at startup is the "GPIO3 Force Power" setting that is missing in the Gigabyte X299 BIOS. I tried to view the hidden settings via UEFI Tool and ifrextract, but it seems that the only settings available are those already visible, or maybe I'm wrong?