Yes, it is a "retelling" in that the events are different, but the events of the rebuilds could not have happened without Shinji already having completed at least one loop beforehand.

In 3.0+1.0 he sees all the different possibilities that have played out on the "movie screen" during the instrumentality portion of the story. He realizes that even if he stops instrumentality that things will just keep playing out the same way over and over again. He chooses a future in which Evangelion do not exist. The angels do not exist.

The reason this was a big step forward is that even though Shinji is scared of politing Evangelion, it has also become his purpose for existing. In deciding to move forward without them, he is forcibly removing his "reason" for existing.

It is heavily hinted at that both Mari and Kowaru are somehow aware of the loops and have several pieces of dialogue that seem to imply this.