Sam, the Sugya in Pesachim is a far cry from a scientific conversation. We all watch the sun going down, and they just felt compelled to say that it goes up? Why is there a Chachmei Yisroel opinion in the first place? The Jews had to set up their own observatories? (Besides, from our perspective it goes North, which is considered up as Rashi explains by the Meraglim IIRC). Also, the old excuse is that they got their science from the Goyim — although they neglected to ever mention that fact, and “Tanya” is hardly an allusion to a contemporary Goy. How does that square with this Gemara?
The salamander is a Mesora. It says it about Chizkiyahu. I’m sure you aren’t saying they made things up. Slifkin mentions in his book that there is a type of newt that can survive a fire for some time by oozing a jell. He then goes on to disregard that and says that he feels like an athiest in doing so. Let’s not confuse what the Rishonim mention with the status the Gemara gives it.
The mice might be about half decomposed mice or it can be about something from hearsay that they decided to discuss. I don’t claim that they knew all science. But their Torah is true and what they were Mekabel from Braysos or derived from them is true.
The medicine Gemaros are indeed what they heard from local travelling merchants. That is acually not followed. The Gemara in Avoda Zara says already that an Amora tried one of them and it didn’t work. Another merchant gave him different advice that helped.
This is what Rav Shrira Gaon is talking about when he says that they are not our doctors. They decided to include contemporary medicine Letoeles Harabim. These are not (at face value, at least) a Kabalah.
You can even find where they Paskened a certain Shayla based on a doctor’s Tevias Ayin, but not a Halacha Ledoros.