I think the main source of the confusion is that the connector is called USB-C, but devices that use the connector may not be USB devices at all, since they can fully expect to only be used with devices that support a specific alternate mode (e.g. Thunderbolt). Yes, they all have to support USB at some level to negotiate the alternate mode (i'm not sure if for USB-C this is a passive signaling like sense resistors or something active like an authentication chip), but devices don't have to fall back to USB data modes at all if they don't want to.

If they had called the connector something distinct, like for example "Omnibus", then you could additionally specify the signalling required to make it work. So you could sell a device as being "USB via Omnibus plug", or "Displayport via Omnibus plug". Maybe even come up with little icons for each mode and place them on the host computers and peripherals to help people figure out what is going to work. Really just anything more than what they've done currently would be useful.