I have created a Scratch animation which was then recorded and tracked. The tracking is successful but I cannot reconstruct it in the 3D environment. Whenever I select one empty or multiple and try linking them to the track, the empties appear at the origin and don't move when I play the animation or scrub through. The tracks on the movie clip editor window move as they should along the track, but the empty in the 3D view window remains static.
It seems that a few minutes of fidgeting solved the problem. I turns out that it is required to have a camera on the 3D environment to properly link empties. That is all that I had to do, doesn't require much of an answer.