You’re forgetting that a large part of the Planescape setting is treating anyone without higher understanding as ignorant Primes. It’s fairly common to associate the same arrogance to the players who prefer the setting.
But when it comes down to it, if two people have conflicting ideas about how something works, at least one of them is wrong. If you have a disagreement about what’s the center of the solar system two common arguments are either the earth is the center or the sun is the center. For millennia we thought it was the earth. We were wrong. For centuries we thought it was the sun. But we were wrong. Now we know it’s a point near the sun thanks to the gravity of Jupiter.
If the cosmology of the planes is an established fact, either the people of Eberron are right or wrong. Either the Planescape notion of cosmology is right or it’s wrong. Both can’t be right, unless we’re going back to crystal spheres and applying that to cosmologies somehow. But both could be wrong.