It's still part of the spec, although optional. You don't not need an extra card, at the most a controller, i.e a small surface mount chip. The fact that the MacBook only have 1 port, makes the need for Thunderbolt more pressing since you can add any port with a breakout box on your desktop.
Yes, a separate chip of some sort - of which the Macbook has virtually no room for. Further, there is little call for Thunderbolt in such a computer, as USB-C already does everything you are stating as an advantage for Thunderbolt within the needs of a computer of this size. One port to a dock with charging, display, usb ports, etc. And to get the extra bandwidth Thunderbolt 3 offers over USB-C/3.1 you need bulky active cables. Thunderbolt is going to be limited to the Macbook Pro lines, I'm virtually certain of it.