This is actually the point where I start to have an issue with the "secret bible". I'm actually just fine with there being a secret book of lore for FR or Dragonlance or Greyhawk or Eberron, etc. In fact, I think there really should be one for each setting. The problem is when someone thinks any of those books has any bearing on any of the others.
One of the really amazing things about AD&D was that it wasn't a unified setting. Yes, Gygax put lots of vague (very vague) lore in the core books and there was a published Greyhawk setting. But Orcus, the planes, Vecna, the Wind Dukes of Aqaa, and so much more were just inspirational building blocks to be interpreted and snapped into your own game. Is Orcus "alive", dead, risen as undead? Whichever suits your game. Krynn didn't need to share a cosmology with Greyhawk (even though there were attempts) because it was a different story that used the blocks differently. Dark Sun didn't have to explain why things worked different; they just did. Yeah, there were some attempts to explain how to jump from one world to another, like Greenwood's articles where Elminster, Mordenkainen, and Dalamar sat around smoking and drinking. But, they weren't particularly canon.
D&D isn't a unified setting. It's actually just the opposite. It's a meta-setting that supports multiple, unlinked settings. There shouldn't be any sort of official attempt to make it otherwise -- at least not in a definitive way. Planescape is fine. So is Spelljammer. Neither exist for me, though.
How does Eberron fit in with Greyhawk? It doesn't. They're two settings that use the same mechanical system to play. It's like if the same company owned the rights to do a Babylon 5 game and an Aliens game and chose to use the same mechanics. You could say that Aliens was a few centuries earlier and that the xenomorphs exist in B5. The system would make it a breeze to do so. But, it sure isn't inherent in anything with either setting.
