I get your point. I think the "Empty Thought" commentary can be either a reference to the Great Darkness, or simply a deeper poking into the Makers own deep inherent fatal flaw. However, it also makes sense to say that this kind of purpose cancer is the potential danger of all cognitive development in the universe and, say, that the Vishnans were very lucky or very careful to dodge that bullet.
So what is fascinating in this Protocol between the shivans and vishnans is how they deal with a simple difference of opinion regarding whether if this species is to be culled or not. It's really an important matter because if the Vishnans have it all wrong and call for a non-cull on an otherwise too narcissistic a species, the contribution of this species (which apparently must be a duo according to Battuta) might pollute the Psyche and bring forth the Great Darkness, thus destroying the entire purpose of the Protocol.
In AoA, the shivans are really not happy with the Vishnan's decision, but there's another assymetry there: only Vishnans can "see" through different dimensions. The Vishnans are, like you say, "guys in hazmat suits poking at things through a pinhole".
They brought the 14th to their dimension so they could directly intervene in them. But their mission failed, which is crazy in itself... Nevertheless, the Vishnans have probably decided that the human's species is a no-go. Therefore the Protocol is clear: the cull is about to be cast, or has already been cast. Shivans are allowed to kill humans / vasudans. But wait, because now the shivan local anima is Ken, and Ken has a different scheme: to use humans as tools of shivans, and thus make them be part of the shivan toolkit. And thus let them live. Because without this kind of "strategy", local cull would already been in effect and third incursion would have already started. Ken is holding the Shivans back with this bargain.
Now, what the vishnans might be thinking or planning or considering here might be interesting, because they might be witnessing a strange pattern in this dimension that was not how they saw things going. Why aren't the shivans culling them according to the protocol? And what is this weird Laporte doing here in Nagari? They still might intervene in order to check what the hell is going on here.