For the few Pro Users who Specifically paid a small fortune for their thunderbolt device - they will certainly know which port to plug it into, there will be zero confusion.
What's nice (awesome) about this, though, is that when Apple/Microsoft/Sony/Asus/whoever decides to differentiate their high-end products by offering Thunderbolt 3 ports that people will rarely have a use for, they can actually make use of them immediately as USB 3.1 ports. Right now I have a MacBook Air w/2 USB + 1 Thunderbolt Port. I have too carry Ethernet Dongles for both Thunderbolt and USB to cover the situation in which I run out of ports and need ethernet. And I frequently run into a situation in which I've used up my two USB ports, and my third adapter isn't thunderbolt (I know, I should carry a Thunderbolt -> USB adapter, but god, I carry so many cables already).
In this new world - I would have three, fully functional USB ports, with one of them also capable of functioning as a thunderbolt port should I have a Thunderbolt peripheral.
Awesomeness.
EDIT: Looks like my assumption is correct: