Linux 3.17 has a commit which supports hotplug of thunderbolt of non-chained thunderbolt devices. But what does "non-chained thunderbolt devices" mean? Is a thunderbolt to ethernet adapter a chained or non-chained device? How about a thunderbolt to display port adapter?
See Apple's promo page for info about Thunderbolt. It also describes how you can chain devices together instead of needing a hub or similar. My impression is that hot-plugging such daisy-chained devices are what are not supported by the linux commit; only single devices, whatever type they are.
Thunderbolt 3 is a beast of a protocol and hardware solution. In Linux, there is some support for Apple devices but nothing very generic currently, as I understand. For instance with kernel 4.9 (Debian 9) with the Lenovo Thunderbolt 3 docking station and Lenovo Thinkpad T470 everything worked if I booted while attached to the dock. Suspend/ resume would not work, just the power and the display would come online. With kernel 4.13 I can reliably suspend/ resume with everything coming back online. I cannot hot-plug though.
BTW the original Thunderbolt is really relevant only on Apple hardware from what I know. Thunderbolt 2 got deployed more widely on Dell and Lenovo hardware in addition to Apples.
Thunderbolt should work as DisplayPort (and in case of Thunderbolt 3 as charger) pretty much all the time. The switch to "Thunderbolt alternative mode" should be easy enough to be supported as one of the first things.