Considering that AMD Graphics Cards can be used behind the Thunderbolt interface I wouldn't be surprised. (XConnect)
If I remember correctly, you'd have to get permission to add Thunderbolt support into drivers....
They would have to license it from Intel. Which I bet Intel wouldn't really want to do.
The standard chipsets do have support for USB 3.1 Gen 2. But mixing in support for DisplayPort would require either a custom chipset (which Apple may be able to do but might not be as cheap), or wait until a Zen-based APU comes out.
USB 3.1 Gen 2 plus display is not the same as Thunderbolt. TB is basically straight PCIE. Can't just combine data and video and call it Thunderbolt. Plus 3.1 Gen 2 is only half the speed of TB3.