The details of the rakia (as understood by Chazal) are discussed earlier in Pesachim and in the Yerushalmi, in terms of its substance and thickness, and are not particularly relevant here. The point is that, according to the Chachmei Yisrael, the sun travels through holes in the rakia at shekiah and passes behind the rakia at night and thereby cannot be seen.
The Shitah Mekubetzes that you referenced is quoting Rabbeinu Tam. And this is exactly what Maharam Alashkar is addressing. Sure, Rabbeinu Tam was of the view that the Chachmei Yisrael were actually correct, and that the sun really does pass behind the sky at night. However, as Maharam Alashkar points out, the Geonim and all the other Rishonim accept that the Chachmei Yisrael were wrong. The sun does not go behind the sky at night; it continues its motion on the other side of the world. And we today know that with certainty.