Do we hold the ancients' reasoning from their evidence to our standard of knowledge? Or do we approach them on their terms and limits?
We know there are not "hooked atoms" and "smooth atoms" but do we applaud them for using their available observations (e.g., fishhooks in a box) and extrapolating a natural explanation of nature, free of supernatural and divine intervention?
I do not see these as contradictory. The evidence hopefully improves with technology, but the analysis process - the rules that constitute how to apply the observations as standards of proof - ought to be (in my mind, anyway) - exactly the same.
I think what you are hearing in recent podcasts is our working toward a way to better articulate this -- and we have quite a way to go yet, I think.
That's why I am personally not nearly as concerned with the specifics of their conclusions as I am HOW they reached those conclusions. So far, I am very comfortable that their "process" is valid, even where they may reach conclusions we today think are "wrong" because we have evidence not available to them
I personally even hesitate to use the word "wrong" to describe this situation.