This reminds me of "if a tree falls in the forest does it make a sound?
Except the forest is in Canada and the people who don't hear anything are in Kenya, and who never cared about the tree in the first place.
Religion in Eberron is gods don't interfere. There are people who worship gods and believe they exist. Because gods don't interfere there are also people who do not believe they exist. Treat the campaign like that, use the Eberron cosmology, and don't have any gods interfering the campaign seems BAU.
This is why I laugh at all of this... those people all ticked about Eberron being a part of the multiverse are blaming the wrong gods.
Not only that, they might want to read page 300 of the PHB. No one should have been surprised by something that was already stated years ago.
"The best-known worlds in the multiverse are the ones that have been published as official campaign settings for the D&D game over the years—
Greyhawk, Blackmoor, Dragonlance, the Forgotten Realms, Mystara, Birthright, Dark Sun, and Eberron, among others. Each of these worlds boasts its own cast of heroic adventurers and scheming villains, its own ancient ruins and forgotten artifacts, its own dungeons and its own dragons.
But if your campaign takes place on one of these worlds, it belongs to your DM—you might imagine it as one of thousands of parallel versions of the world, which might diverge wildly from the published version."
Eberron existed in the 5e multiverse before
Eberron: Rising from the Last War was published. It also only did so solely at the discretion of the DM.
Elves ORIGINATE from the Forgotten Realms.
Officially.
No, they don't. The demi-human gods exist in multiple worlds other than FR that also preceded FR. They are not a part of Eberron. The elves of Eberron were created separately from the elves of other worlds as a race of elves free from those influences.
Elves existed before FR and in worlds that existed before FR.
Ahm. Did you involve yourself in Eberron cosmology? I did never dm Eberron or play it pen and paper but i am a long time ddo online player and ddo is Eberron at its finest. It got a cross over route to FR in the game via the Demonweb, and to Greyhawk via portals, and a possibility to get to ravenloft via the mists, adding some classic DnD modules for all those settings.
DDO bases the cosmology on Eberron, but we can see some unexpected influence. Running the quest chain to get to FR demonstrates the existence of the Silver Flame as a sentient force more than I would have ever expected in PnP campaign, for example. Getting to Greyhawk quests, FR, or Ravenloft is also more open than the typical Eberron PnP campaign (IME) as getting into those other worlds violates the normal level of separation.
Eberron is one of my favorite campaign settings. I really don't think the option to include or exclude it from the D&D multi-verse has any bearing on that at all. DDO is fun to but it doesn't handle that aspect quite the same way.