The problem here is that we have a complete clash in tones between Sigil and The Great Wheel.
I think I see what you're saying here, but my understanding is that Planescape's Great Wheel is no more the same as Greyhawk's Great Wheel than the Twilight vampires are the same as Bram Stoker's vampires. There's plenty of similarities, but there's a lot of very important differences that means that they're being ultimately used in very distinct ways in each of those treatments.
Admittedly, I think D&D has tried to conflate the treatments of the Planes and Planescape in 2e, in 4e (as the World Axis), and now, it seems, in 5e, because in each of those e's there's One True Cosmology. I don't think that helps things. But as it is played, and as I have played it, these are distinct things.
Sigil (pre *spit* Faction War) is a war of competing shifting philosophies. What you do, even what you argue, matters. Philosophies can rise and fall - and even be all but wiped out. If the Mercykillers were to decide that the whole of Sigil was impure and start cleansing it that would be a problem. If you were to somehow engineer a merger between the Takers and the Heartless (not that difficult in some ways) and drive the Dustmen underground you would fundamentally change the nature of Sigil as it stands. This is IMO sensible.
And quite fun!
The Great Wheel is a war of immutable symmetric philosophies. The philosophies are opposed - but due to the symmetry of the wheel, Balance Is King. In two Great Wheel settings this has been made explicit; the Avatar War started because the Gods forgot that Balance was King and in Dragonlance himself Palatine says that the goal was to free the pendulum, and that Good held sway just before the Cataclysm, implying that was the cause. In Great Wheel settings, Gods represent their philosophies and those philosophies must be upheld by the God. The God isn't the power, the God is a minion of the Great Wheel and they can be put on trial for not fulfilling their function. Strike one down and they will be replaced (which is why we've had multiple Mystras).
IMXP, as PS is played, this isn't the case. While it may be true in certain D&D source material such as Dragonlance and Greyhawk and FR (I know less about those settings), PS don't roll that way. The Great Wheel is explicitly mutable (The Third Layer of Arcadia, sliding gate-towns), and gods aren't reflections of the Great Wheel as much as they are reflections of the people who worship them (because belief in your divinity is what turns you into a god). While an individual character may regard balance as king, the PS setting itself doesn't regard that as true in any meaningful way. The Great Wheel itself is explicitly pointed out as as "only a model," only as true as the people that view the world this way take it to be true.
This is part of why I'd make a distinction between PS and the Great Wheel, ultimately. When you've got a game about leaping between infinities, mapping explicitly becomes a matter of perspective.
Because balance isn't king, your point about good being pointless isn't necessarily true (though certainly you could have a character that believes that). I think the more setting-relevant challenge to the set-up of an orphanage isn't that the cosmic scales will balance somehow, but rather that the question arises: why does my character think that setting up an orphanage is a capital-G Good In A Cosmic Sense thing? It matters to "that starfish," but if that starfish is going to grow up and perpetuate the cycle of poverty and war that creates the need for orphanages in the first place, maybe my act isn't as good as I like to think it is. Maybe being exposed to the horrors of abandoned children is what it will take to sway people into peace?
An orphanage in Planescape might look like a celestial raising children to be child crusaders, or a demon playing nursemaid to scarred orphans of the Blood War to get paladins and priests to protect it against the hellbound assassins tracking them, and the players get to ask these questions of themselves: when does this cross a line? And how? Are both bad things even though they are both functionally useful orphanages? Are both fine because they are orphanages regardless of what else they are? Is one good and the other not? Why?
Good isn't pointless there, but the idea is that Good means different things to different people and ultimately it is the PC's version of Good that transforms the multiverse, it is their ideas that, over the course of 20 levels, should emerge to define Good for people across the planes. It's not a direct accounting of balance (well, maybe if you're a rilmani, or maybe a modron, but those are explicitly alien beings of immortal thought), but rather a questioning of the nature of the thing.
Jam the two together and there's a huge clash in tones. The only reason Planescape/Sigil works at all is that there is an Overgod (the Lady of Pain) who has this one city as her personal petri dish and is simultaneously as curious and disinterested as any good scientist in seeing what happens. Sigil is the only place in the whole of Planescape where you can change anything important - and that only because of the protective umbrella of the Lady of Pain insulating Sigil from The Great Wheel.
Again, I don't think this is true on a setting-wide level. PS is a setting where gate-towns slide and where layers shift and where changing ideologies re-shape the cosmos. It is explicitly a game of a
mutable Great Wheel.
It's possible that other D&D settings find the heavens less mutable for one reason or another, but in PS at least, things don't stay the same.
I'm of the opinion that Planescape works better with the 4e default cosmology than with the Great Wheel. The World Axis is inherently unstable, and the Great Wheel, as I've argued, promotes evil and makes good pointless.
I think ultimately for PS that cosmological maps are kind of irrelevant (which is why I had a pretty solid, if brief, 4e run in the setting), in part because of that flexibility. The World Axis can be true alongside the Great Wheel and alongside, I dunno, the Egyptian understanding of the path of the Sun, and they'd all be compatible with each other,and you could have three different characters in the party who all believe their own version of the tale and could even run a coherent PS adventure where all of them receive confirmation of and denial of their world views.