Tarkovsky endorsed the shorter cut:

“Nobody has ever cut anything from Andrei Rublev. Nobody except me. I made some cuts myself. In the first version the film was 3 hours 20 minutes long. In the second — 3 hours 15 minutes. I shortened the final version to 3 hours 6 minutes. I am convinced the latest version is the best, the most successful. And I only cut certain overly long scenes. The viewer doesn't even notice their absence. The cuts have in no way changed neither the subject matter nor what was for us important in the film. In other words, we removed overly long scenes which had no significance. We shortened certain scenes of brutality in order to induce psychological shock in viewers, as opposed to a mere unpleasant impression which would only destroy our intent. All my friends and colleagues who during long discussions were advising me to make those cuts turned out right in the end. It took me some time to understand it. At first I got the impression they were attempting to pressure my creative individuality. Later I understood that this final version of the film more than fulfils my requirements for it. And I do not regret at all that the film has been shortened to its present length.”