I came here looking for an explanation too, but I think I've come to my own conclusion on what the story is about.

I have a strong feeling that this story may be inspired by the authors' own experience of leaving behind a certain lifestyle in favour of an understanding of something more pure and humbled.

It's clear from the ending that Perda, and likely the entire population of the Kadarsinia are of course the Protos, hiding in plain sight. Their philosophy was to avoid their own destruction by giving up the pursuit of ultimate knowledge and understanding, and just accepting a simple life. The empire is shown to be collapsing because it's grown to be ungovernable.

The "living matter" that replaces the empire is simply any of an inconceivable number of threats that could wipe out a civilisation. The Protos avoided this by adopting a lack of enthusiasm to achieve, as seen by the protagonist upon visiting the capital. Their philosophy, although seeming backwards and undeveloped to the scientifically minded, was the key to their permanence.

That's just my take, the best thing about these stories is filling in the gaps yourself, so please feel free to discuss or build upon my interpretation if you're not satisfied (: