No godly interference. They are subtle, not just placing a shield.

Plus it was in place that the Draconians and the Humans were related, not the Equestrians and Humans. Faust may have connected them, but she didn't create the humans, nor did she ever do anything with them other than a language similarity. The Draconian-Human relationship went on before you made up all the Fauust-and-human stuff.

The Supremes will look down on Equestrians; they will watch and occasionally insert themselves into human re-evolution.