Maybe, could change the Hydaelyn systems version of Mars to whatever planet Omega came from instead. We know that exists and it leaves the original question fundamentally the same.
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The big issue with this question is that we cannot know, because the devs do not know.
Even internally, Square Enix has yet to fully commit to the degree to which the universe is messed up. One of the things they were discussing more recently was, "Okay, if Omega's homeworld and the Dragonstar are both in traditional space in the Source's dimension, were there fourteen of those planets, too? Or is this a local phenomenon?" They don't need to make a decision until it's plot-relevant, but they know it's causing fans to scratch their heads.
As far as they've thought about / confirmed it so far, it's a local problem, so your "spaceship to a common destination" question is one they'd probably want to consider for when the time comes, lol.