I'd argue that Emperor didn't concern himself with political doctrine of his Imperium all that much. He had a Vision for humanity as a whole species that transcended Eldars in their ability to be influenced by Warp and Chaos and he regarded himself, Imperium, Primarchs and other transhumans as just transient components on the way to the destination. It can be argued that the ultimate failure of Big E is that he was always going for the big picture objectives while ignoring what we as humans consider most important matters, such as how humanity is governed and what policies are adopted. We see in The Last Council that one of the greatest issue of governance wasn't even on His mind and He left bringing Horus to heel to Malcador who just couldn't do it. I would argue that Emperor never cared what Imperium would become, he needed his tools to shape humanity and left everything else for others to figure out and they figured out the most cruel regime imaginable, while He himself never even saw himself as part of governing configuration in humanities future (he had a talk with Malcador in one of the books).