I’m not sure if this is related to any of the problems you reported, but on the BIOS updates page I can see for the upcoming 3.03 version they list one known issue as “System cannot recognize Thunderbolt 3 devices after resuming from S4.”
I wonder if that also applies to the current 3.02 BIOS and could explain at least some of your issues?
The BIOS/Firmware update page is here: