And the USB 3.1 "SuperSpeed+" PHY is a 10Gbps thing that is very comparable to Thunderbolt electrically and would be expected to evolve similarly.
You're right that USB lacks the PCI framework (which many of us view as a feature). But DP/Thunderbolt similarly lacks a cabling standard with the sophistication of USB: no charging, not reversible connectors, no OTG-style switching of host/guest mode.
Apple had a choice of supporting both connectors, or giving up "PCI madness" or "nice cables" to get just one. They picked USB.
Supporting something like Thunderbolt is nice, but not exactly the same. It's not about "brand identity," it's about "does this equipment I have work with this machine?"
So, can the Type-C connector support Thunderbolt? Yes. Does the Type-C connector currently support Thunderbolt? No. Will someone add Thunderbolt over Type-C? Maybe.
I've only heard of PCIe over Type-C (via the spec docs) and DP over Type-C (from the VESA guys).
And thank goodness they did.
The "U" in USB may finally become reality. It's overdue.
Displayport is a protocol that can run over a thunderbolt port, but the thunderbolt spec includes much more than that.
I don' believe we'll be seeing the 40Gbps PCI extension that is today's thunderbolt over USB 3.1.