Not scenes.If taken to its logical conclusion I find this argument quickly becomes absurd. Is Star Trek: The Motion Picture in a different universe to TOS? After all, it changed the look of virtually everything from the Enterprise herself through to the Klingons, introduced the concept of a warp core as a fundamental component of warp drive and reversed Matt Jefferies' original intent that nacelles were self-contained engines and power plants, and all but reversed any character development Spock had in accepting his humanity. Is VOY in a different universe to TNG because it retconned the whole history of the Borg and the Federation? Is the TNG episode "The Host" in a different universe to DS9 because the nature and look of Trills are different? Where does this end? Are individual scenes we don't like to be consigned to alternate realities?
Camera cuts.
It's the only way to fix issues like Spock and McCoy swapping uniforms in TMP, or Robau's badge vanishing and reappearing in ST'09.
Every shot is an alternate reality, and we're watching a clumsily put together sequence of similar realities.