It's a multiverse, therefore there are infinite numbers of everything. There isn't just one Demogorgon across the D&D Multiverse, because if there was... I could call WotC up right now and tell them my players killed him, and they would then have to remove Demogorgon from any piece of literature in the future. But they don't do that, because there isn't. My Demogorgon isn't theirs. Just like it isn't yours.
Same way the FR gods don't exist in my Eberron, because my Eberron is my Eberron and any 'canon' is merely from the perspective of someone else. If someone else thinks that the FR gods exist in Eberron because another person made the choice in their game that they did and now they have to accept this 'canon' as their own... that's on them. I choose to not give one whit about canon because it is pointless and goes against the definition of a multiverse in the first place.
A multiverse is infinite. That means there are universes where Demogorgon has been killed and ones where he hasn't. As well as worlds where the Demogorgon is the one like in Stranger Things and not the two-headed Demon Lord. And universes where the gods of Eberron are real entities, and ones where they aren't but the people there all believe they do. And ones where people know they aren't real and instead have just personified concepts by turning them into "deities". And indeed universes where people from Eberron have Plane Shifted out of Eberron and gone to the FR and met the FR gods.
It has all been done and none of it has been done. And thus I find there to be no reason to worry or bother with it. All that concerns me is what happens at my table, the rest can go flake off as far as I care. As I said... worrying about any of this is overrated.