"I don't understand" - or do I?

The discussion about disputes over approach/ content being misleadingly labeled as disputes over "tone" began with Rabbi Seinfeld's comments to an earlier post, when he made statements such as the following:

In these discussions of Torah and science, is anything lost by pointing out a stira between science and a maamer chazal with those humble words, "I don't understand this Gamara"?
To do so doesn't sacrifice one iota of critical thinking - nor does it sacrifice kavod.

In a post referencing my response, R. Josh Waxman made the following excellent comments:

I would say that the person he is responding to is being silly. It is not a matter of mere tone to refuse to come to a conclusion. And saying "I don't understand the gemara" is not the same as saying "I understand the gemara in accordance with the Rishonim that Chazal can err in science." This is no mere difference in "tone." It is unfortunate that "frumkeit" and false modesty make people believe that they are not allowed to think.

And meanwhile, if one refuses to come to a conclusion out of piety, there is little to no chance of making use of a conclusion. And understanding that, and how, Chazal made use of contemporary science is potentially extremely useful in coming to understand the correct peshat in countless gemaras.

Furthermore, so many of these non-rationalists are under the mistaken impression that saying Chazal relied on contemporary science and thus erred on occasion detracts from Chazal. In fact, it is just the opposite! I have greater respect for them for this. They did not close their minds to evidence and to knowledge from secular sources, thinking that scientific statements about the world from centuries past were Divinely given. Rather, we see from explicit examples and many implicit examples that they looked to contemporary science. They believed in Torah UMaddah on some level! Which we rationalists respect greatly, even as some non-rationalists do not. That occasionally, or frequently, this led to adopting mistaken positions is no reflection on the piety, or the intelligence of those who held these up-to-date scientific positions.

And it's appropriate to see how Rav Hirsch approached such topics:

In my opinion, the first principle that every student of Chazal’s statements must keep before his eyes is the following: Chazal were the sages of G-d’s law - the receivers, transmitters, and teachers of His toros, His mitzvos, and His interpersonal laws. They did not especially master the natural sciences, geometry, astronomy, or medicine - except insofar as they needed them for knowing, observing, and fulfilling the Torah. We do not find that this knowledge was transmitted to them from Sinai.
Nowadays too it is enough for the non-specialist to know about any of these areas of knowledge whatever contemporary experts teach that is generally accepted as true. This applies to the lawyer vis-a-vis all other areas, to the mathematician and the astronomer regarding the natural sciences, and to the expert on flora regarding all other areas. We expect none of them to seek out the truth and satisfy his inclinations in any field other than his own specialty.
Moreover, even in the area where one is an expert, it is neither possible for him nor expected of him to know everything through personal investigation and experience. Most of his knowledge rests upon the investigations of others. If they have erred it is not his fault. It is sufficient and praiseworthy if his knowledge encompasses all that is accepted as true at his time and place and generation. The greatness of his wisdom is in no way belittled if in a later generation it is discovered that some of the things he maintained or accepted on the authority of others are unreliable. The same is true for Chazal in these areas. The greatest of them knew all the wisdom and science of all the great non-Jewish scholars whose wisdom and teachings became famous in their generations.
Imagine if a scholar such as Humboldt had lived in their times and had traveled to the ends of the world for his biological investigations. If upon his return he would report that in some distant land there is a humanoid creature growing from the ground or that he found mice that had been generated from the soil and had in fact seen a mouse that was half earth and half flesh, and his report had been accepted by the world as true, wouldn’t we expect Chazal to discuss the Torah aspects that apply to these instances? What laws of defilement and decontamination apply to these creatures? Or would we expect them to go on long journeys to find out whether what the world has accepted is really true? And if, as we see things today, these instances are considered fiction, can Chazal be blamed for ideas that were accepted by the naturalists of their times? And this is what really happened. These statements are to be found in the works of Pliny, who lived in Rome at the time the Second Temple was destroyed, and who collected in his books on nature all that was well-known and accepted in his day.
The Talmud in Bova Kama declares “A human spine, after seven years, turns into a snake; this applies only if he did not kneel at Modim. “ Anyone who reads this finds it laughable, but Pliny says the same statement almost word for word, “After a number of years the human spine turns into a snake.” Chazal, however, used this to teach a mussor lesson. To any mind it is clear that every similarly surprising statement of Chazal, if we look into it, was accepted as true by the scholars of the time.
We find that Chazal themselves considered the wisdom of the gentile scholars equal to their own in the natural sciences. To determine who was right in areas where the gentile sages disagreed with their own knowledge, they did not rely on their tradition but on reason. Moreover they even respected the opinion of the gentile scholars, admitting when the opinion of the latter seemed more correct than their own...