I don't have a fixed line for what level of scifi is acceptable in my games. Back in 2E, even before the revised boxed set came out, my Dark Sun campaign had a subplot foreshadowing the upcoming invasion of biotechnological space halflings, which apparently was something TSR was actually considering for the official line.
Barring out of context scenarios, like an alien invasion or the return of not-Atlantis, what matters to me is that blending of different elements makes sense in the internal logic of the setting, otherwise it feels like the 60' dragon waiting in the single entrance dungeon room at the end of the 10'x10' corridor.
I like Eberron because I can see the effort that went into making sure all the bits and pieces fit organically in the setting, but Revel's End/Prisoner 13 (from what I read in the other thread, haven't actually played it) gives me more of a tone dissonance with the rest of the setting and it feels like it would break my immersion. Admittedly, it's mostly a matter of taste where the line falls.