One thing I wish they did to further differentiate the two universes is have Applejack’s parents alive in the EQG verse. As far as I’m aware they never established any rule where someone’s death in one universe would cause the same thing to happen in the other. I think it would make an interesting story if Pony AJ traveled to the human world and ran into them.
You are right! Circumstances are different between worlds, ergo her parents may be alive.
Edited