Huh. A theory just occurred to me.
In reading the second original post of this discussion thread, a dusty nodule was sparked. Here we go:
Humans were the original dominant species of Earth. Everything was the same as it is today; city-life, automobiles, nuclear weapons, coffee, etc.. However, there was no Sasquatch - they were just another variation on the ape. Over time, they evolved to a point at which their intelligence grew equal to humanity's. With that unrestricted ignorance and violence, they were able to wipe out our species, including most of the Foundation - most of it. They continued to evolve over a few thousand years, and in a way, they regarded the Foundation-in-exile as the Foundation views them today. That coincided with the benevolence to the now-neanderthal-like human society, essentially continuing with the tone of the article. Following this few-hundred years of "peace" the Foundation were able to create SCP-2000, in an effort to reboot humanity.
The Foundation, or at least one of the 05 council members, was collectively the deity that armed the humans and induced the SK-dominance shift. The reason that the Foundation does not know what SCP-2000 is is because the events of SCP-1000 instituted it, whether accidentally or intentionally.
I guess it's just cool to think about.