From what I've seen in this subreddit, feudalism is now thought to be a bad way of thinking about medieval European society.
But one common feature I've seen is that governmental control was decentralized to a great extent, and there were many levels of organization that made it possible to, for instance, be a vassal of two different kings at once who actually ignored both of them. The Church was also a parallel government authority to the secular state.
Was this "multilayered sovereignty" more present during the medieval period in Europe than before and after? Or is non-multilayered sovereignty just a feature of modern nation-states, and medieval Europe was just normal in this regard?
Can you clarify what you mean by multi-layered sovereignty? Are you asking if it was common for people to live in a territory where they were subject to the laws and customs of multiple overlapping sovereigns? Aside from the example you noted of the Church authority being a parallel to the secular state, I can't think of many examples to illustrate this, other than occasionally disputed border territories (like parts of France during the Hundred Years' War). Can you maybe name some specific regions you're asking about?