Miracles can - by God’s sovereign permission - be worked by others than God, so miracles by themselves prove nothing; they certainly do not prove that the miracle-worker has a Divine commission. Men can feign them, as can demons.
Critical Biblical scholarship is a service to the Biblical texts, with the intent to make sense of them. I cannot think of any undertaking that is more authentically Protestant, more faithful to the highest priorities of the Reformation, more perfectly in agreement with the efforts of the Protestant Reformers to uncover and elucidate the true meaning of Scripture, than that. That the results of such scholarship may be very disconcerting, is not in the least surprising. Theologically and religiously, it is immaterial whether the Book of Isaiah has 1 human author, or 2 or 3 or 12 or 20; or whether St Paul wrote 14 NT Epistles, or 13, or 10, or 7, or 4; for God alone remains the Primary Author of all Scripture.
In glaring contrast to that, Fundamentalist Evangelicalism is not only a betrayal of salvation by faith alone (in the sense intended by the Reformers); it is also a betrayal and a rejection of their attempts to discover the true meaning of Scripture in all its bearings. Fundamentalism has been a catastrophe for Protestantism, not least because it has led to a situation in which the errors of Fundamentalism are charged against, not Fundamentalism alone, but against all Christianity without exception. The Trumpolatry of US Evangelicalism is one of the fruits of the pathological sickness of Fundamentalism; for it was never, at bottom, a Christian movement; it has always been social conservatism masquerading - perhaps innocently, at first - as a Christian movement.
The waters in Gen 1.6 are are “the waters above the earth” that, on occasions, come down through the sluices in the solid firmament of heaven, the upper surface of which is where God is enthroned. That surface is a solid pavement, of (IIRC) lapis lazuli. The precise location of the heavenly sea, in relation to that solid pavement, is uncertain. That is what the Biblical texts say, so that is what must be accepted as the Biblical picture. Later readers, such as ourselves, have no right whatsoever to distort the texts by making them more “scientifically reasonable”, for to do that, is to pervert Scripture - which is the very crime of which critical scholars and critical scholarship have so often been accused. That Biblical cosmology does not agree with scientifically accessible cosmology, is totally irrelevant to what the Biblical texts, taken in the literal sense - that is, the sense intended by the human authors - are supposed to mean.
If the meaning of the texts, accurately interpreted, is contrary to the doctrines of either historical Christianity or of Fundamentalism, then so be it - what matters, is not that the meaning of the texts should support Christian or Jewish doctrines, but, that the texts should be interpreted as accurately as possible. If that leads to the destruction of every Christian doctrine ever taught, then so be it.