Shorting Thunderbolt Card Header:
We've found that for the most complete hotplug functionality, shorting the card is usually required. This information especially applies if the user desires the ability for the card to initialize on boot
without any Thunderbolt device connected. We dive into Thunderbolt hotplug configuration
In Our Guide. Shorting the cable is also neccessary if you have a motherboard which does not support Thunderbolt cards, although you may have more limited functionality as the card may automatically initialize with security type SL1, possibly interfering with the ability to mount devices.
If no hotplug capability is desired, shorting is optional although may produce better results on some motherboards. Attempt to connect via the header, and if your card is not detected by macos consider a short. If you choose not to short the Thunderbolt Header Cable on the card side, you will need to plug your Thunderbolt cable from your card into the supported header on your motherboard.