I think a big theme in your post, and one that I think is misguided, is to see the difference between upper and lower as a physical difference. It is a thematic difference, and I think treating each sphere as a formless blob with no content is detrimental.
Celestial magical sphere: Linked to stars and the sky, maybe be related to the movement of the stars, the time of the day, definitely related to the "star" that is how Galbarian mortals see the sphere.
Chthonic magical sphere: Related to earth, likely more telluric in nature, if a mage in the former case would raise his hand to reach for the magical realm, this one needs to connect with that which is bellow, walking bare-feet, channeling magic through the body, whatever.
Celestial soul sphere: Probably Heaven or Valhalla like, angels and Valkyries, sky burials and funeral pyres
Chthonic soul sphere: Hades for example, boatman and reapers, crypts and graves.
There is a big change, and that goes beyond portals and physical place.
Since one appeal is that everyone can design their own Sphere to be the source of its own 'magic' and have its own effect, I think forcing sweeping things like this to be the case would be detrimental even if they help unify the Upper/Lower Spheres thematically.
One thing I expected in the docs, but couldn't really find, is a model of what you are thinking. With examples, models, something like a few example spheres and how they interact. It clearly isn't the Aristotlean model what we are doing here, there is a weird mix of Aristotles like layer spheres and orb spheres, and each time these things are discussed, I go out of it knowing less and less, with mixed messages like "There are no exceptions except the exceptions"
It is better to have a complex system that deals with its issues than a nebulous unclear system. I think if you want a strong thematic difference between Celestial and Chthonic, you need to at least state that and what you overall view on what is Upper and what is lower. Once the themes are put on the table, we can discuss them properly.
I'm interpreting this as you saying that examples are warranted, yes? I intend to add quite a bit to the Doc today and could give 5 or 6 such examples.
Speaking of which, I still think land gods are a problem, from what I see, the Chthonic realm is way too limited, and throwing trees to the sky because of canopies is... eh. I don't know crap about the nordic myths since I found them boring, but in terms of Aedra/Deadra, all Aedra would be Celestial, and... most of the Deadra as well, since they are outer gods, Azura, Clavicus, Hircine, Vaermina.
It also makes the metaphysical maps of the world weird, with the realm of rives, trees and the fairyland all side by the side with sun, with the stars. It makes sense in a world like Tamriel where all worlds are outer worlds, but is this what we are going for here? Weren't we going with Aristotlean layers, with a realm of wind, a realm of fire?
See, what you say about trees is due to one very poor example that I gave. The example in question was a forest god's Sphere perhaps being the upper canopy of some jungles, but back a page or two age when we chose to go with option B we more or less killed the idea of ta forest god having a Sphere like that. It's just too accessible, too tangible, too real. As the Spheres are partially metaphysical and magical places, that's why I think BBeast gave really good examples with the sky god's Sphere being the upper sky but great storms making it hard for just anything to fly up, and the dirt god having a Sphere that's underground but can only be reached by digging a long, long ways beneath some sacred hills.
To clarify, in keeping with the theme of Spheres being very magical places that are hard for mortals to access, I don't want someone to just claim "deserts on Galbar's surface" or "the rivers on Galbar" as their Sphere. Something more along the lines of the desert god having the sun (or perhaps some fiery subterranean realm) as his Sphere and then connecting it into the depths of deserts through some sort of portal is more of what we're going for. Instead of just claiming rivers as his Sphere, a river god could do something like claim the subterranean depths where all springs draw their water from.
Do you think that I addressed your confusions/objections adequately, Capy?