I'm not certain how to address the other parts of this beause this part has left me somewhat baffled.
It's possible we have a misread situation. I'm referencing stata, which is a regression analysis computer program:
https://www.stata.com/
As for the methodology he's using I find most of it to either be obviously in best practices or above my personal ability to evaluate. Some of the index adjusting that you're referring to is empirical. House effects adjustments are based upon actual results vs. projected results of the poll across multiple election cycles. Other adjustments generally have a similarly empirical basis. Some of these are very sophisticaed. Silver had an article recently about measuring polls accuracy when they're going against the grain of conventional wisdom. As a general rule, I find it difficult to believe his model is significantly weighting non-statistically significant factors. Also, anytime you make your name in two different fields using statistical modeling at such a young age and with a high degree of accuracy in both fields my general assumption is that he's frankly better at it than I am.