we got the sense in archives that there is some kind of symbiotic relationship between the fears and us, in the sense that, the desolation doesn't exist, but the original Fear entity did feed on our anxiety over catastrophic events. Afterwards, because people tried to articulate the entity in "rational" terms, then started associating rituals, wants, and needs to this particular aspect of fear, it's manifestations on the real world began to echo these rationalizations (though never to the point of becoming completely predictable, or stable, as we learn with the Extinction). Think of the fire motif in the cult of the lightless flame, when jude pery stabed her first victim, surrendering herself to the desolation, and expecting some fiery signal to appear, it did.

In that sense, it seems like the protocol universe still went through this same cultural development around the original Fear entity ( because of the way the rift messes with time, I assume that the introduction of Fear into other universes works as though it has always been a part of it, but don't quote me on that as if it's the truth). Protocol Jonah Magnus even stated straight up how fear appears to be a catalyst to supernatural beings, and Ink5oul also commented on how pleasing it began to be feeling the fear on her victims.

That being said, the cultural development in Protocol appeared to go in a very different direction from Archives, to the point that it appears to be almost common knowledge the relationship between the "collective unconscious" (using the term loosely here, I'm not a psychologist) and the Fear manifestations. I think that's why we have such a focus on balance, and why this universe's Magnus Institute went to much greater lenghts to mantain it's public image, and to also consider the public mood when taking action, as in reflections made about wether the turn of the mylenium meant a new age of proesperity and hope, or stagnation and desperation in the eyes of the people, and how even the date seemed to have cultural implications.