Autochthon is already the Special Primordial because he's the one who 100% sided with the Incarnate Rebellion, made the Exalted, and has been handed credit for countless other things.
You're really confusing twee "Specialness" with "has a defined role in the backstory," and I think you honestly have a bigger axe to grind with that latter part of unwanted focus than
really making him conform to what everyone assumes the primordial condition entails. Besides, I never said that only the Yozis have the tiered soul-structure, just that Games of Divinity called-out it for them exclusively in the context of "the organization of the Demon Realm," and no indications have been given in any direction
but the briefly-noted state of Autochthon that this was or can be meaningfully changed.
The rest of your post is honestly just griping that everything defined about Autochthonia, even in nutshell format, doesn't hew hard enough into your established model for "how things should work." Look, I understand you've had a lot of success with this Infernals stuff, but it's not the only possible game in town. One Primordial, out of two-dozen odd Yozis fitting your qualifiers for "distinctive," a handful of unspecified dead ones and one wildcard, showing that unbroken primordials do not have to be so aggressively defined by a specific soul layout to the exclusion of all other factors and characterization, is not an inherently bad concept, no matter how much you insist that this is the sole-interesting aspect to be found. Hell, claiming "their minions have minions!" is the
only meaningful distinction to make for Exalted's primordials compared to literally everyother mythological or fantasy titan out there is the most reductionist shit I've read in a long while.
The setting is a kitchen sink, its concepts can exist outside of the box you personally built to contain it.
Games of Divinity gives nothing to indicate that the soul hierarchy was something forced on them by their imprisonment and that'd be a pretty important detail.
Demon-summoning and the Surrender Oaths, as I mentioned. The three tiers of demons exist in GoD because the spells were written in the Corebook, and the relevance tied to the Yozis came after. So this means one of two things in-setting: either the bindings of the oaths arbitrarily split all denizens of the Demon Realm into three neat classifications, or that soul-structure is a notable element of the Yozis themselves, mentioned nowhere else except as an allusion to co-location tricks. Even Gaia, the only other free primordial, has never had any of her sub-souls mentioned beyond the Five Elemental Dragons, and even that is a crap-shoot definition depending on which books you take at face-value.
The Yozis are repeatedly referred to as primordials, but not every primordial need to fit the ironclad definitions cast onto the Yozis by everything that places them in the context of "being in hell." Personally I think that's better for everyone, since it allows Malfeas to sit on its niche of codified demon-summoning relevance, without demanding everything else try to ape it with none of the established backdrop for why that shit even exists in the first place.