"The belief its natural forces all the way down is just a belief." ... but rationalists can't admit that. They have to reject both philosophy and theology (metaphysics) in favor of physics. But as you point out, physics only deals with observable post-Big Bang phenomena .... that and the dogma of Uniformitarianism ... that the laws of physics are the same everywhere and at all times (at least since the Big Bang) or at least outside of Black Holes. But this is a claim "to far". We have very little data on the interior of stars or ultra dense objects, and none at all of the inside of a Black Hole or the earliest part of the Big Bang ... nor are we every likely to, from observations made at least from within the Solar System, in any conceivable historical time.
If you know GR well, then you know that a meter isn't a meter and a second isn't a second, except in the immediate vicinity of a given clock/ruler. Not just because of moving frames of reference, but because of gravity. So if Uniformitarianism is true, it is nuanced. That and these "variations" led us correctly to believe that matter can be changed to energy and vice versa (because non-Euclidean 4D geometry). If you really want to know if a meter is the same here as it is nearer the giant Black Hole at the center of the Milky Way, then one has to journey there. It may be rational, it may be probable ... but it is unproven. This is what has led to the missing Dark Matter and Dark Energy that vexes modern cosmology. But then cosmology has never been an experimental science ... unless we can become trans-dimensional mice ;-)