The two answers provided by Jeroen and Orny are good, informative answers that are perfectly accurate. Websites can certainly track you with these sophisticated tracking mechanisms. Whether they actually do this is a different matter. There's little incentive for them to do so since the majority of users aren't using incognito mode, or other means of preventing tracking via cookies. Setting up this more sophisticated tracking would take an effort to enhance the existing mechanisms for a small return.
Remember that most websites only want demographic information, they aren't terribly interested in making sure every last person is tracked. The ones that are interested in tracking behavior and what you're interested are also still going to be interested in the 99% who aren't using tracking blocking means, not the 1% that are.
The NSA obviously is very interested in individuals, and has the people to be able to do this more sophisticated tracking. I'm sure they're particularly interested in tracking TOR users who are trying to remain anonymous.