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This makes my brain hurt:

Thunderbolt 3 is really an “Alternate Mode” use of the Type-C port/cable, just like HDMI. But in practice, Thunderbolt 3 is a super-set of USB 3.1 for USB-C since no implementation of Thunderbolt 3 will be USB 2.0 only.

Anybody care to explain?

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"Alternate Mode" means "use these same pins for something other than USB". So Thunderbolt 3 uses the same connector but re-purposes the pins and wires to carry 2 or 4 PCIe 3.0 lanes rather than USB. HDMI similarly repurposes these pins to carry traditional HDMI signals.

Anyone implementing Thunderbolt 3 will also be implementing the full USB 3.1 stack in the same chipset. Intel, for example. It would be silly to implement just Alternate Mode Thunderbolt and skip the USB 3.1. That's all I meant.

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