I think it’s fine for us to not know much about something. We don’t have all the answers in the universe, we’re just hairless monkeys after all. I just wish more people would be accepting of a “that’s complicated, nobody really knows and you’ll have to try a bunch of stuff to see what works for you specifically” approach.
To your question, I am slightly above the prescribed line in a lot of metrics and don’t really do anything special, I am lucky enough it doesn’t have any impact on my life in general.
I like the way you put it, it’s okay that we don’t know everything, and you’ll have to try a bunch of stuff. That really is at the core of what I was trying and failing to say. :) We don’t actually know how gravity works, but we use it anyway. I made an analogy to PID controllers in another comment, maybe that’s a better way to describe calorie I/O; PID controllers know nothing about the thing they control other than it’s output, and yet they are an extremely useful tool.
My wife reminded me of a book that might interest you and might have pointers to some of the research you’re looking for. “The Secret Life of Fat: The Science Behind the Body's Least Understood Organ and What It Means for You“ by Sylvia Tara.