I don't think Susano was a Primal, of course we think of him as such but he didn't actually show any Primal characteristics while manifest in the world. He never hungered for aether since he never consumed other Kojin relics that probably held aether as far as we can tell. He never drained the land of aether, no Kojin were tempered, while there was faith in the kami as a whole that is not the same as beckoning your specific god to intervene, the Kojin only seemed to know his name after he announced himself. Yes, Lyse and Alisae said that he was a Primal, but they never took any actions to confirm that at all, no checking with an aetherscope, just the panicked assumption that Susano was a Primal.

So then what was he? I have to take the Kojin at their word for this, I think Susano was a Kami made manifest. Why shouldn't the Kami be able to take physical form? What rules prevent them from doing that? This doesn't mean that Susano wasn't a threat and had to be dealt with, he was and we did. However it does mean that our understanding of spiritual phenomena is less comprehensive than we thought and biased in favor of just shoving all manifest beings under the umbrella Primal and not understanding that this may be a different phenomena altogether that looks like a Primal manifestation to the unobservant.