The question is how to mix them ,Humm maybe we could make it so its where Rapture opens up to the world finally sometime in the Fallout timeline the reason it finally opened up the place was nearing the breaking point in the structural area as the splicer had keep the population up and not really inbreeding without too much trouble over the centuries by periodically taking others from the surface but now those of rapture must go to the surface.
While those of the Equestrian version of Columbia Bioshock shows up for some reason like maybe to counteract the trouble of the splicers now on the surface .
Speaking of these things did you note there was mlp references in fallout 4 and there was a atleast implyed reference to bioshock infinite in MLP heres a vid to show you of the mlp scene in trade ya
https://www.youtube.com/watch?v=U6YVpKp5k2Y if you need I can link you to a vid of where fallout 4 seems to reference mlp