Eberron scholars are unsure -- and have no way to discover -- whether the Eberron deities (Sovereign Host, Dark Six...) have a real existence or if their follower just power their spells out of their own faith. They know that the Silver Flame physically exist, but can debate, as far as I understand, whether the Silver Flame is a godlike thing or just a Couatl-created magical creature.
The physical existence of FR (or Greyhawk, or Greek) gods somewhere in the multiverse doesn't impact the rightness or wrongness of the Eberron scholars, since they are not debating about these gods (whom they have no way to even learn the name), they're debating about the Eberron gods and worship.
In my opinion, the claim that Aureon, Balinor or the Traveller are real isn't validated by the existence of Cyric in an unreachable part of the multiverse. And the claim that the same gods don't exist isn't proved wrong by the said existence of Cyric...