Jer said:
Since I like both Eberron and Planescape, I'd keep them separate - like I did with the Dark Sun material. Eberron has a really unique cosmology where the gods do not physically interact with the world at all.
Eberron's cosmology is nearly indistinguishable from the Planescape cosmology in every respect that matters. I know that sounds like an odd thing to say, since Eberron has only 13 outer planes to Planescape's 17 outer and 18 inner planes, but I don't think the precise number is important for anything other than reiterating the "Baker's dozen" theme that crops up all over the place in Eberron. If other planes existed, the setting wouldn't be substantially different.
If you look at the individual planes, Kythri is essentially indistinguishable from Limbo, Xoriat is the Far Realm, Daanvi is essentially Arcadia, and so on. It seems distasteful and messy to me to fill the multiverse with doppleganger outer planes with nothing in particular to recommend them. Why have two identical Limbos when one will do? If they were uniquely interesting in some way, that would be one thing, but they're not - Eberron's planes are pretty generic, designed for maximum compatibility with generic planar monsters.
Both Planescape and Eberron have orrery-based cosmologies, although Planescape was vaguer about this.
As for the gods, that's just a matter of the style of the campaign. Either the gods throughout the multiverse are interventionalist (and definitely exist) or none of them are. Either style could work with either Eberron or Planescape.
I'm not convinced that making Eberron theologically agnostic or imprinting the number 13 everywhere are themes interesting or important enough to justify bend the multiverse into knots.
Dragonlance Adventures was very vague on the matter of the planes, and it's a mischaracterization to say it definitively presented a separate cosmology. If you read the "Travelers From the Beyond" section on page 12, it's clear that it's possible to get to Krynn from other AD&D campaign worlds.
There's no particular reason why Krynn's inhabitants should be thought of as especially ignorant. They call the planes by the names they prefer - that's a cultural difference, not a knowledge-based one. Every culture has its own names and diagrams symbolizing the planes of existence, and while some are more complete than others, none of them are "wrong." Sigil's maps of the planes aren't necessarily complete, either. Personally, I care less about what Tracy Hickman thinks than almost anything in the world, except possibly what Keith Baker thinks.