From the sources in my monograph The Sun's Path at Night, we see that all the Rishonim, without exception, as well as many Acharonim, accepted that Chazal believed that the universe is a solid dome above the earth. (Most of the Rishonim themselves adopted the Ptolemaic view that the universe is in fact a series of nested crystalline spheres surrounding the earth, while some maintained Chazal's view.) There are other passages in the Talmud where Chazal discuss the thickness of this dome and other aspects of it, which, again, all the Rishonim, without exception, accepted as a literal discussion of the physical universe.
From where we're standing, there is no reason not to believe that all these Rishonim and Acharonim were correct in their understanding of Chazal. I won't say that it is "incontrovertible and irrefutable" that Chazal believed the universe to be a dome, because nothing is incontrovertible and irrefutable, even the idea that the world is round - there are always people who will controvert it and convince themselves that they have refuted it. But I will say that I do not believe that such an approach is at all rational. The fact that some later authorities were uncomfortable with the idea of Chazal having such beliefs is not reason to say that all these Rishonim and Acharonim were incorrect.
But here's where we move to stage two. Chazal's belief that the universe is a solid dome was not merely their understanding of the universe. It was also their understanding of the Torah. Throughout Tenach, there is mention of the rakia - the firmament. It was this that Chazal explained to be a solid dome. R. Yehudah HaNasi only rejected the idea that the sun passes behind this dome at night - he did not reject the idea that there is such a dome. Even those Rishonim who rejected the Babylonian cosmology still subscribed to the notion of the heavens as a solid dome over us - it was just that they understood the heavens to be a sphere rather than a hemisphere. And this is not just a matter of how Chazal translated words in the Torah, but also how they understood phrases and descriptions in the Torah, such as the account of the luminaries being placed in the firmament, and of the heavens being stretched out over the earth, of the windows in the firmament through which things enter, etc., etc.
In a later post, I will discuss what these Pesukim mean from a modern perspective (please wait for that discussion, and do not raise this topic in the comments). The important point to recognize for now is that Chazal (and most of the Rishonim) universally interpreted various words in the Torah to be describing the heavens as a solid firmament above us. And yet, nobody today believes that such a structure exists.
Malbim was sensitive to this problem. In his commentary to Bereishis 1:6, Malbim rejects the view that the rakia is a solid firmament. He argues that it refers to the atmosphere - an argument that we shall analyze in a later post. Malbim acknowledges that all the Rishonim believed it to be a solid firmament, and declares them mistaken. However, he claims that the Sages were also of the view that there is no solid firmament, citing R. Shimon bar Yochai as saying that the stars move through the air. But this is deeply problematic. First of all, Malbim does not adequately deal with all the passages in the Talmud which speak of a solid firmament (his novel explanation of Pesachim 94b is not shared by anyone else at all). Second, the words of R. Shimon bar Yochai cited by Malbim do not exist in our version of Bereishit Rabbah 6:8, which reads quite differently; apparently Malbim had a corrupted text. Third, even if R. Shimon bar Yochai did speak of stars moving through the air, this in no way denies the existence of a solid firmament.
Chazal and the Rishonim believed in a solid firmament. People today do not believe in a solid firmament. Thus, people today interpret the Torah differently from how Chazal interpreted it, based on the discoveries of science.
There are many ramifications of this, but there is one in particular that I wish to highlight. Many young-earth anti-evolutionists are fond of speaking about "How the Days of Creation Were Understood by Our Sages," arguing that Chazal and the Rishonim did not believe that the universe was billions of years or that life evolved. In this, they are absolutely correct. However, there are two critical points that they miss. First was that many of the Rishonim certainly saw it as their duty to interpret the Torah in accordance with what science or philosophy had proven - even if that meant going against Chazal and against the literal reading of the Pesukim. Second is that even these young-earth anti-evolutionists are going against Chazal and the Rishonim in how they explain all the citations in the Torah about the rakia and shamayim. Our ba’alei mesorah have always understood and insisted that the rakia is a solid firmament, and yet these people disagree.
Oh, the irony!
(At this point I would like to express my appreciation to all those who made a donation for my monograph The Sun's Path At Night, and to issue a request to those who downloaded it without making a donation, to please make a donation.)