I suppose something that incorporates what you first posted would be something like....
The multiverse is a series of crystal spheres, which only spelljamming vessels and deities can travel between normally. Outsiders and the like must otherwise travel through portals linking the astral plane of one crystal sphere to that of another, or somesuch thing. Within each crystal sphere is an astral space and several 'prime material disks', inner plane disks, or outer plane disks. Dunno how the ethereal plane and plane of shadow would fit in. Maybe each material disk has its own little ethereal bubble overlapping it, and perhaps behind the fabric of the multiverse is a plane of shadow, linking material disks with those of other crystal spheres, but unchartable, unlike the phlogiston or whatever between crystal spheres. Or maybe it is the stuff of the plane of shadow through which spelljamming vessels travel?
Spelljamming vessels and portals are used to travel between the various inhabited disks of each crystal sphere (though some portals may just lead the astral space, and then a traveler would have to search for another portal in the astral that leads to their intended destination). Travel through the astral space without a spelljamming vessel or a direct portal might take vast amounts of time; it may seem to be an infinite distance between material disks, without a spelljammer to keep the astral space from stretching or fluctuating along the way.
Each disk would be like a flying saucer in shape; wide, thin, slightly curved on top and bottom; mortals and the like would live on the top and bottom surfaces, and each disk would be sufficiently separated from the others to develop different cultures and races, even from related influences. Yet with portals and spelljammers, and deities that want to spread their faith and missionaries, the disks would still have some interaction. Deities, planar disks, crystal spheres, and other things would spring up from the force of mortal beliefs; once enough mortals believe in something strongly enough, the malleable forces of the multiverse bend to their will in some way and create things from that mortal faith.
In part this would be due to the Oversoul (see the recent issue of Dragon Magazine) or something, a remnant of the great mind that first developed in the void and shaped the rudiments of planes and life-forms in the distant past. Over time it became less distinct and more a part of its creations, going into dormancy as a minimally-active, formless, hardly-noticeable force in the fabric of the multiverse. As mortals developed on the first planes, their beliefs shaped deities and spirits from the void and the Oversoul's essence, and these deities and spirits sought to grow more powerful and influential, to spread the beliefs that made them across other planes. Things grew and sorta spiraled out of control from there, until a whole multiverse had developed with all kinds of different races, cultures, magicks, and strange things.
Since deities and outsiders are generally composed of faith and soul-stuff, they embody beliefs and philosophies rather than actually generating belief themselves, for the most part; they don't so much believe in things, as they simply act in accordance with the nature of the beliefs that created them. Thus they attempt to spread those beliefs among mortals, who can alter reality if enough are convinced to believe the same thing, and thereby strengthen the deities/outsiders and further the reach of their faith, that which created them and gave them purpose.
Over time some of the most capable and wealthy organizations in certain material disks gained prominance across the material disks of several crystal spheres; having acquired control of many spelljamming shipyards, they naturally came to have influence in many places and develop strong control in some of those places. These would be things like certian noble houses, guilds, factions, or the like. The home disks of these organizations would be the main places of interest across the multiverse; nations like Thay, Calimshan, Halruaa, and such may be very important and even take up an entire material disk each, due to being lead by one or more of the great houses/guilds/whatever. Other places may be unique or interesting, and important, simply from lacking any major involvement by the great houses and thus being open territory for other people to turn into opportunities.