...all evidence to the contrary.
I'll agree there's a limit to how much you can "pull out and replace", but in this case we're talking about maybe two or three doctrines with virtually no utility, and no applicability to 99.99...% of science, knowledge, and industry. I know evolution especially is a great god on a hill for some atheists, but aside from some implications to phylogeny, and some fantastically contrived arguments about how the theory "helps" bioengineering, it has no predictive power, no consistent axioms, no industrial or commercial utility, no observable implications in non-geological timeframes, and more holes than Swiss cheese shot through with an Uzi. In fact, I'd argue its sole utility is that many atheists believe it disproves the Bible. Ergo its "great god on hill" status and militant orthodoxy.
Ipse dixit.
This I agree with.
To be precise, I don't believe any student is "misled". I think they know perfectly well the difference between taking something from scripture and taking something from empirical observation. However, I do think they need to learn that in some contexts, such as school exams, they just have to buckle down and say, "The exam wants the answer based on the current scientific consensus and not scripture. So be it." Such is life.
I would point out, again, that 99.99...% of students pursuing post-graduate studies are going to go into fields where it doesn't matter one whit whether or not they believe in evolution, the Deluge, etc., but otherwise, yes, I agree that "scripture says so" won't fly at a university.