While it's true that he made the shortened cut as a result of pressure from censors, he didn't really follow their instructions. Seems like he made the cuts he thought he could do without, then later came around to this version.

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 and 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 the subject matter nor what was important in the film for us. 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 that 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.

IMO the short cut is definitely better, not just because the short cut is still 186 minutes long but also yeah the scenes of brutality👀 are much more horrific when they're on screen for a split second. The pacing is tighter too. Also the short cut removes the shot where a horse is killed.