Apple does however control which Thunderbolt devices work with Apple hardware and software. Which means, for example, that Thunderbolt 3 hardware released prior to the launch of the new Macbook Pro is effectively Windows-only: http://plugable.com/thunderbolt-3 This appears to be an entirely artificial software block done to force manufacturers to go through their certification program and presumably give then a cut; there's a hack out there that bypasses it.

That's not true. First, for example Dell's dock works fine with the Mac, second the chip is not Apple's but from Texas Instruments and the non functioning devices are not compatible with this chip. So Apple blocks nothing and devices don't have to go through any Apple certification program.

But these devices work with the new MBP in Bootcamp/Windows just not in Sierra...

>presumably give them a cut.

You just made this up. As already clarified in this thread, Apple doesn't own Thunderbolt and Apple gets zero (0) licensing fees. There is no "cut".

Apple doesn't own Bluetooth either and yet they have strict control over which accessories (gamepads) can be used with iOS and charge for the privilege. Headphones with the old 3.5mm jack are also available in more expensive variants with the MFi certification.

Even when there's no money in it, Apple uses whitelists in some places, like which SSDs get TRIM and which displays work and get the HiDPI checkbox:

https://support.apple.com/en-us/HT206587

Who owns a standard doesn't seem to matter at this point.