They probably should come up with some way to simply mark things though, so you can easily tell by looking at what you're plugging in that everything is good.
Many USB 3.0 ports have blue inner connectors to indicate that they're 3.0 ports, and some USB ports will have yellow connectors instead to indicate a variety of things (from better charging rate to supplying power even when the host device is powered off). I think the logical extension of this would be resistor-style color code bands to indicate different sets of functionality (yellow for Thunderbolt, red for charging, etc.).