I think you are confused because you think in terms of what happens in one universe has to follow a single time line. This is not how thing work in the games. Instead you should think of it from the perspective of a person that traveled through the universes such as the MC, Amelia and Rebecca. They all have their past and that remains constant for them. Whatever happened to them cannot be changed in their past. In the "good" ending (I don't really like this term, for me it's more like a "loop" ending) WW Amelia merges with SO Amelia, has a son and that universe remains unchanged - Megan hijacks M.A.L. causing Amelia, Jack and the MC to try to escape (where SO starts). This doesn't change anything for the MC, Amelia and Rebecca that are left behind in the WW universe. Even if something changes in their original universe it would not have any effect on them because any change would've created a different timeline which would have nothing to do with them.
The "bad" ending (or the "linear" one) sees them getting to a new universe that Megan chose for herself. She has sent the redhead and the MC to a specific time in a specific universe but Megan took a "detour" - went back to the SO universe, merged with Amelia, hijacked her body, married Jack, made Lana's life hell (she's Jack's daughter, so Megan essentially became her step mom), and then used Jack to build the machine and went to the same universe that she had sent you but a few years earlier, so she could prepare for your arrival - comission the ship and send it to the right place at the right time for you to get there. Now, if you think in terms that changing the events in SO's universe would have an effect on the people who got transported out of it and into WW's universe, this would create a paradox. Not necessarily for you, or Amelia, or Rebecca, but for Megan. After all Megan hijacked Amelia's body by merging her consciousness with Amelia's, married Jack and then if by changing her past, she changes her future, this would mean that she doesn't go in WW, doesn't build the new machine, doesn't go back in SO, so... couldn't change the past, right? A paradox.
Just think of everyone's time as linear for them. Up until this point in the story the MC, Amelia and Rebecca had a common timeline but Lana had another - she arrived in the WW universe some 20 years before you three, so for her it was different. Now you are the one with a different timeline than the rest - Amelia and Rebecca got to the station, figured out where and when you would arrive and traveled to the same universe but in an earlier point in time, so they can get to you in time and save you from the redhead.
