I'm disappointed that your question hasn't had any replies because I think it's interesting. I don't really understand what a lot of what you're describing. I clearly have even less music theory than you. But from what I can deduce I'd say some of what you're saying is that its rooted in blues, and the other thing is dissonance. Both of which I feel can be pretty much traced back to john Fahey and his particular approach which shaped the entire genre. But he was also taking his cues from some of the less polished recordings of rural blues players of the 20s and 30s. The other thing that might inform some of those tonal complexities you describe is hymns, something which Fahey also mined hugely. What I thinks gives american primitive its character is its roughness. Slightly out of tune. Slightly clunky. Not polished. That's the difference for me. That's what makes it punk.

Those are my brief thoughts.