After Effects also has a clone stamp tool.
You can use motion tracking to drive the clone brush position and in this way remove the track marks.
This is reasonably easy when the areas around the marks are quite large and/or uniform in texture. If they are not, it becomes much more complicated, because you also have to animate the sample point to keep sampling from an area which is similar in color/lightness. Pesrpective changes in the car can be really painful. If perspective stays locked, a fixed sampling point can be used easily.
I'm also looking for a color matching process that allows me to make two different layers more alike.
Basically I have 2 shots of the same subject, but as the lights changed a little from one shot to the other, those 2 shots have slightly different hues.
It would be great to have something like that "Match Color" adjustment that Photoshop features.