My problem with the Crystal Spheres was always that it's a one-size fits all approach to something where even by TSR's own publications was not one-size-fits-all (Mystara, even while Spelljammer was published, was not in a Crystal Sphere, and yet it had its own rules for space travel).That is disappointing to me. I was hoping they would find a way to eliminate them. They always rubbed me the wrong way.
When I care about making the lore work within my setting (which is sometimes, though not always, but often when I run a world hopping game), the Universe of the Crystal Spheres is one of the possible Universes that have connections to the Ethereal. It's an "infinite" universe (like our own - so maybe it just stretches on infinitely or maybe there's an outer limit but it's large enough to be treated as infinite for our purposes) filled with phlogiston instead of vacuum. And within the phlogiston float the Crystal Spheres which contain various "systems" (though not all are solar systems, of course).
Mystara in my view sits in its own infinite universe as a "parallel universe" to the Universe of Crystal Spheres that is more like ours (space is a void, stars are other solar systems, etc.) and is connected to the Ethereal but isn't connected to the phlogiston. That matches the actual "canon" of Mystara as published by TSR back in the day. IMO Eberron would also be in its own "parallel universe" within the Ether. (As would Athas - I know canonically Athas is in a Crystal Sphere but IMO it really shouldn't be given how much they work to keep it cut off from the other worlds via planar travel). And then whatever other parallel worlds I want to stick out there can have their own cosmologies as well, but are all connected via the Ethereal.
(My Outer Planes also sit within an infinite Astral Sea - the Great Wheel is a specific group of planes that depending on my mood are either artificially strung together via gates because of the philosophies of the Factions of Sigil that think they should be connected in a precise wheel of Law and Chaos and Good and Evil, or are fundamentally connected together that way for some unknowable reason. But there are an infinite number of other Outer Planes out there to be explored that have no connection to the Great Wheel at all - reconciling my desire to use the Planescape planes but also to use the cosmology as set up in BECMI D&D where the Outer Planes were infinite and ultimately unknowable. I'm all about maximal flexibility with this kind of stuff).