To add on to what Mortis said… Think about it yourself. The Twisting Nether is physically separate from our reality, moving through the dimension of time in our reality in no way means you’ve traversed spacetime in another reality that is physically separated.
It does indeed lead to a plothole though… Branching timelines would mean multiple copies of these characters would then exist in the Nether due to its separation from our reality, regardless of our branched timeline their souls would all be sent to the same Nether.
This is exactly why I hate time travel, no one does it right.