When we venture beyond observational science into the more speculative realm of origins, whereby to extrapolate backwards we must make assumptions about uniformity (constancy of speed of light, assumptions about decay rates, assumption about original parent-daughter ratios to name a few), we necessarily must cross that blurry boundary between science and philosophy.
My own opinion for whatever it's worth is that the proper disposition for the observer, a human being living within a miniscule sphere of space-time, is one of great humility. This we can derive from the vastness of the universe, and from our self-awareness - something which does not lend itself well to purely mechanistic origins. We would do well to remember that ancient adage that God resists the proud and gives grace to the humble, and are justified in using that measuring rod (humility) in evaluating others.
Fair enough. I think many scientists are very humble, awestruck by the vast magnificence of what they're studying. (Some are not, of course, and some of those tend to dominate the media. But that's true in any discipline, including religious ones.) But I'm still not sure how that attitude is supposed to affect their practice of science, particularly what you've called historical science.
Take the people described in the original article here. Leaving aside the unnecessary confrontational anti-creationist presentation, how were they supposed to conduct their research and discuss their results? They obviously accept the theories of evolution and an old earth. They looked at the evidence so far and said, "If the theories are right, there should be an animal with these characteristics in the timeline right about here." They looked for it and found it. They presented it as further evidence in support of their theories. What should they have done differently? How would their a priori presupposition of the supernatural change things?
You've criticized, among other things, the assumption of uniformity that underlies such things as radiometric dating. And yet different methods of dating have been shown to produce consistent results, and scientists working with the assumption of uniformity have been able to make predictions that bore fruit. Should they stop trying to build a narrative of origins based on that assumption because there's a chance it might be wrong? Or present all their results with an asterisk and a "*This might all be wrong, if the speed of light used to be different and radioactive materials used to decay faster" disclaimer?