I don’t believe that Eberron is incompatible with the Planescape universe. The planar portals represented by the moons could easily open onto their equivalents in the Planescape multiverse - and there are distinct equivalents.
Regarding Dark Sun, it is the total (almost) absence of access to the outer planes that make Darksun unique. If the planar conduits existed as normal then it wouldn’t be very interesting. Incidentally the inner planes very much do connect with Athas. So I don’t see how it can be irrelevant.
Ultimately the good news is that Planescape has become so subsumed into the core game that it is pretty much a given now. I don’t think the question will ever be will Planescape ever languish.
Its more a question of whether Sigil will be concentrated on, in the same way a desert themed adventure, or cosmic horror adventure might.
I’m always disappointed when people try to remove alignment from the planes though. Limbo, Hades, Elysium, Mechanus and all the permutations in between are both interesting and evocative.
eberron does not have "equivalent planes"
- Daanvi, the Perfect Order
- Dal Quor, the Region of Dreams
- Dolurrh, the Realm of the Dead
- Fernia, the Sea of Fire
- Irian, the Eternal Day
- Kythri, the Churning Chaos
- Lamannia, the Twilight Forest
- Mabar, the Endless Night
- Risia, the Plain of Ice
- Shavarath, the Battleground
- Syrania, the Azure Sky
- Thelanis, the Faerie Court
- Xoriat, the Realm of Madness
Edit: There is a simple solution that lets you mix the two however. Sigil was made by the dragonmarked houses at some future point in time after starting to explore a bizarre new & disconnected set of planes they found. Thanks to the back & forth of time when crossing planes it could even be made in the distant past by the distant future. Like Arcane (whom the houses can also almost seamlessly fill the role of in secret) they are happy with you not knowing who made & pulls the strings behid those that seem to run it. Of course the critical difference there is that planescape undergoes minor changes that allow nearly everything about planescape other than who made sigil, if someone is pulling strings in sigil, & critically if there are one or more spheres not connected to the great wheel planes due to having some other set of planes to remain as is rather than forcing other settings to change their lore with it.