Welcome back Ativan, glad you are posting again. I'll get back to you later tonight if I can to sharpen your points. I think we fundamentally agree, but how we get there is where differ.
More later, but I just want to make a preliminary remark in that all scientists conduct their research within a framework of natural causes with no attempts to appeal to the supernatural. That's why they must assume all causes are empirical and naturalistic.
The questions you are raising are philosophical, which isn't the concern for scientists. Science cannot understand itself.
I'm not sure I understand why you place such importance on separating philosophy and science, and calling attention to their separation. No science could be done without a thousand bricks of philosophy acting as a foundation. Perhaps half these bricks are beliefs and assumptions so common that we don't even think about them as philosophical, we just take them for granted without thinking of them at all. That science should work on curing cancer. Why? What if you believe as Christian scientists do? The overwhelming majority hold to a very different belief about such matters though, so that position is simply ushered right in and past the line and bouncer. Another is that we should try to test and confirm data. Why? For verification? Yet as journal articles multiply we end up with situations where there are a bazillion claims being made, and on a great many of them you can find conflicting data, competing hypotheses/ideas, and contradictory conclusions. So why not wait until we reach critical masses and then do experiments? As opposed to the 'publish or perish' system, where getting into some graduate programs takes into account if and how much you've published, getting tenure often makes a good publishing history a requirement, and so on? It's a philosophical position. The who do science and those who set the course of it prefer one method over all the other options. They prefer to let a bazillion articles be published in ten thousand journals, half of which might be completely fraud, and a large portion of the other half being largely useless or even harmful. Of course it's hard to change now--mid stream--but it's still a philosophical brick.
There are others that are perhaps still controversial among a larger group. Once the group reaches 'big enough to lobby the government, or bug us' status they usually can get some kind of acknowledgement. Animal rights, for example. Is it right to experiment on animals? Mammals? Rats vs. fish vs. cockroaches vs. chimpanzees? We can't use chimpanzees to test out new drugs to be used in death penalty cases? Why not? Well can we still kill single-celled organisms? Where is the line drawn, and why? Or another line of questioning: is it ok to do experiments that are not seriously harmful (death or vegetablizing), but not ones that will effectively end the life? Is it ok to do dangerous experiments on humans? If sometimes, when? Only if they are terminal? As long as they give their consent? Never, if it has a more than 10% chance of killing them? Who decides, and how? Is there a non-philosophical, scientific way to figure this stuff out? One of the common criticisms of sola scripture is that there is not table of contents included by God from the start. Well, is there a list of oks and not oks from the start with science? Does some non-philosophical experiment demonstrate why cadavers are now allowed to be used for all manner of scientific investigation, including (fittingly but morbidly) observations about the effects of weather patterns, wild animal involvement, and the like on dead human bodies, such as how fast they decompose in this or that condition.
Why spend billions on going to space? Searching for this and that? What direction? Why talk of humans going to Mars? What are the arguments between scientists about? Specifically the ones that are competing for the grants that make most of the experimenting feasible? There are arguments about which would yield the most data, which would give the most accurate results, and so on. But the great majority of them are straight up philosophy. Let's focus on mining random objects in the solar system because there's money in them there thingers. No, we should focus on learning how to keep one of them from slamming into earth and destroying the planet; in fact, we should be doing this urgently. Nah, the chances of that happening are miniscule; it is my opinion that the chances are so small that we should focus on other, more productive things instead, like how to protect astronauts from the negative effects of being in space. What? Humans shouldn't even be in space! And so on and so on, in just that one area.
Before, during and after science does science, it must also do philosophy. Or, scientists must know and do philosophy as a part of the scientific method, and it's in many cases more integral and foundational than the would-be factual, naturalistic, non-philosophical stuff. I don't know what you'll think of this, or if I have completely misunderstood your point. Anyway, I hope I didn't write this for nothing. Oh wait... Har har, couldn't resist.