I think the OP's point is that we should understand our current models of natural phenomenon to be just that, models. Outside of their predictive capabilities we should remain humble about how much "truth" they contain and be skeptical of their ability to tell us what's "really going on".

Kepler and Newton's models produce better predictions over a long period than Ptolemaic models, which is great. But it's a bit of delusion to think that necessarily means they are analogous to the cosmological mechanisms that produce orbital mechanics.