You make a fine point, but because of the limits set on gods in D&D (even they look up to Ao who doesn't talk to anyone) there is still room to make these same sorts of arguments on science vs. magic.
What really interests me with this sort of discussion is the attempt to fit something to the given data (which is what science is in reality) as a kind of thought experiment. It is also useful in universe crossover battle discussions (the lowest form of nerd argument I'm sure, but fun nonetheless).
Mostly I just like asking "How does that work?" and since I have my own world to use as a yardstick, that is where I start.[/quote]
Well, when it comes to Ao it's a little more complicated than that. If you remember at the end of the old Avatar Trilogy Ao reports to his boss just to "blow your mind" however I seem to remember that they covered this basic heirarchy in the old basic D&D Immortals Rules which seemed to be used as a basis. The basic idea being that if your running a campaign where the characters have ascended to Godhood, there needs to be things bigger than they are (requiring 'parties') and the various universal level threats that they apparently contend with in the backround. There were levels above your basic "god" pretty much as described in the books. It's been a long time though.
That said when your dealing with something like a Sphere Of Annihilation it's more or less just a magical item which a deity (or sufficiently powerful wizard, though easier for gods) can create. I seem to also remember a couple of them control Spheres like puppets to use as a weapon in Avatar form (but I haven't used D&D in any form for a while so I can't remember which ones). The exact process hasn't ever been put down I don't believe, but at a guess it would involve basically either creating a small portal to one of the planes of Entropy or taking a piece of that so called "planestuff" and crafting it into a sphere, and then adding whatever it takes to move the portal/blob of planestuff mentally. The whole entropy concept coming from again very old D&D Immortals rules, where the gods empowered by entropy are apparently trying to bring about the cessation of reality. This leading to deities of various alignments with regular spheres of influance fighting them. Again this isn't scientifically plausible, but uses a magical logic.
As far as the specifics of the game system, well a lot of it was based heavily on vintage sword and sorcery. One of the problems even with 1st Edition AD&D was that it worked under the assumption that anyone playing was familiar with the basic concepts taken from those books. Leading to debates and misinterpetations on how terms like "Lawful" were intended to be interpeted since the whole idea of Law/Neutral/Chaos Good/Neutral/Evil (just the former in basic D&D) was based on Michael Moorcock's books. Likewise spell memorization was taken from Jack Vance and it was assumed you were familiar with his writings for some of the explanations of why things worked that way. Of course things have moved away from this over time, but still you can see signs of the foundations from which it was all built. I get a sort of wry amusement from people who write essays about why things work the way they do in D&D (such as the basis for old spell memorization systems) without realizing where the idea was ripped off from for example. Or lengthy descriptions (some actually in the core books nowadays) of how alignments are supposed to be interpeted, with no understanding of Moorcock's multiverse or how it was intended (ie ripped off). D&D was very much intended as a plaything for fans of the fantasy of the era in which it was created.
At any rate, trying to figure things out by current physics is kind of pointless. By the same token applying real physics to magical effects (of which I've seen various examples of over the years) usually tends to limit mages heavily, especially in most adenturing groups where they have a hard enough time already (very weak at low levels, and at high levels everything that they can fight is usually so loaded with magic resistance or has such good saving throws due to it's level that you pretty much need a gimmick for everything to begin with).
If you start going into Spelljammer as Canon, I mean even the way "space" works is entirely differant. Your solar system could actually turn out to be being juggled by a giant jester or something equally bizzare, bringing to mind images out of some acid inspired cartoon like the old "Yellow Submarine" or whatever.
I suppose if you use OLDER definitions of things like say putting Blackmoor in the past of the D&D Known Worlds, and then using "normal" space and the whole plotline involving "The City Of The Gods" (ie Crashed Aliens in a space ship), or the 2E "Tale Of The Comet" campaign, you could start argueing for some scientific elements. But even then, magic is all about altering reality, not playing by it's rules, which is what puts your fantasy adventurers into those scenarios as a major force (even the non-spellcasters being loaded with magical gear by the intended level).