It would take some fancy writing to get the Mortis story to mesh with the "mundane" level plotline. For instance, as already pointed out, the Dark Side can't be ascendant in AOTC because the Daughter wasn't dead yet. At worst, there might be some feeling of disturbance in the Force as the Father weakens.
I'm not saying it does literally mesh with the overall plot line, or that when AOTC happens it's literally at the same time as the Daughter's death. I'm saying that the events on Mortis are a compressed retelling and foretelling of the Star Wars saga, like a stage-play or interactive retelling of the prophecy.
Mortis is not something that will have literal impact on the events of the galaxy. It's a warning and a foreshadowing. I wouldn't be surprised if after the Son is killed next episode (not a spoiler, just a guess) that everything will fade to white and our three heroes will wake up on their shuttle in space with their clone buddies calling them from their cruiser, wondering what's going on, with mere seconds having passed in real time.
