Does the "clear meaning" of the scriptures trump science?

First of all, it seems like you’re insinuating no one could know what Genesis 1 means because we don’t know the original language, or that those who don’t know Hebrew can’t understand God’s Word. That would be an “interesting” view of inspiration and preservation, so I hope that’s not what you mean.

Yes, it does matter. But I have to be responsible for my own thinking both to God and to myself. And appeal to authority is a logical fallacy.

I came to a realization that Genesis 1 refers to steps of creating new things out of other “stuff” that was there before in most of the verses. Then I had the thought that maybe “waters” was all the matter in the universe. I looked up what a mash of matter would be and an article said scientists believed the universe started out as quark-gluon plasma. (Funny to find out months later that John Gill thought “waters” was also all the matter in the universe over a century ago). Yet I just assumed that “waters” maybe was just liquid, and maybe there wasn’t another word to use for liquid in ancient times. Then I kept getting farther into science and realized that the heavens were mostly made of dark matter, and we can’t see it exactly (transparent like water), and dark matter could be liquid. Then I realized the separation of the waters on the second day meant that some of the matter referred to on Genesis 1:2 is in the heavens. I looked up all the verses about “heaven of heaven” and many referred to the waters. Everything I was thinking about science and Genesis kept coming together. And since radiation and electromagnetism can be combined into the electroweak force, and electrons can be turned into photons and God creating light would “power” everything on, the “waters” of Genesis 1:2 could not contain electrons if they were also part of “light.” Therefore the waters in Genesis 1:2 could reasonably not be H20. It might even be ruled out.

To be sure I was being faithful to the Bible I looked up the word for waters. And considered various passages Strong's Hebrew: 4325. מָ֫יִם (mayim) -- waters, water I searched for the word liquid in the Old Testament to see if I was wrong and the verse should have included a different word - my assumption on inspiration being that the writer would use the word with the clearest possible meaning. None of the words translated “liquid” made sense there that I could tell.