But I suspect the new understandings will also reflect a great deal of what we currently call Mysticism. Particularly of the ancient variety - not the wannabe brand honed by massive hits of acid - but those of philosophers from ancient cultures that seem to have some very common themes. Fritjof Capra's "The Tao of Physics" is a classic along this theme - which sought to liberate physics from the vestiges of a classically mechanistic view of the universe.
I suspect you're right, owing to the fact that there are so many flavors of mysticism, and so many of them are so vague, that surely one of them can be stretched until it looks like the new physics, regardless of what that physics happens to be.