You're getting too tied up in brand identity and going too far in the other direction. What we call "Thunderbolt" is effectively an evolution of the DisplayPort PHY (which already supported graphics streaming of course, and also encapsulated USB transfers) with protocol extensions to do more PCI-like transactions.
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.