Can't speak for whichever model you have, but I had the gen3 4x SFF-8643 model. It definitely didn't have hotplug implemented correctly. It seemed to only have one hotplug slot when it should have had one for each downstream port.
If you can boot into Linux, do a `tree /sys/bus/pci/slots` and check `/sys/bus/pci/slots/*/address` to see which ones correspond to what. If you can't, then you can check in hwinfo64 and you should see something like this for each port:
View attachment 44066
You also need BIOS support for hotplug events. Fortunately, Thunderbolt has forced most manufacturers to start supporting hotplug events.