The "alternate universe" thing is simply a changed premise based on more modern scientific theories.
By going back in time and altering things Nero created a divergence point in the timeline. The timeline was
the Prime one until it split. It wasn't previously existing, like "In a Mirror" (which would have created a split in the Mirror Universe when Defiant arrived)
By "old" Trek time-travel rules STXI would have erased TOS (which is probably why Warped9 wants to "prove" this couldn't be the case). By the new, based on real-life
theories (no matter how bizarre it sounds) every trip back in time creates a new branch on the timeline tree.
Most of prior Trek can, just about, fit into this system (albiet impractically). Thus Janeway didn't "undo" anything in the Voyager finale, she just created an alternate timeline where events unfolded differently. STIV returned not to the future they left, but to one where two whales and a research biologist were stolen and a whaling ship was was spooked.