As to "[religions] deflecting the scientifically minded's favourite mysteries to magical agency", well, I agree with the late Arthur C. Clarke that magic is merely sufficiently advanced technology; but as far as I can tell, the favourite mysteries of scant few of the scientifically minded are the mystical ones! Those anomalies are usually swept under the carpet by pathological scepticism tarted up with some seemingly scientific credentials.

People will see what they want to see (or as someone said, "seek and ye shall find"). Here's a typical example,
...we now have quite solid grounds (e.g., the recently released Benson study at Harvard) for believing that intercessory prayer simply doesn't work.
Apparently Professor Dennett is unaware of three decades of research by the (recently terminated) Princeton Engineering Anomalies Research (PEAR) program, among other research.

Limited though rational, scientific inquiry is, it would have taught us a whole lot more but for its flawed, human practitioners — scientists with egos, empires, grants, tenures, reputations, ideologies etc. to protect and enhance. Recently we discussed the problem of compartmentalisation along the lines (if I recall) that highly specialised research is impenetrable and that cross-pollination is difficult. But as I see it, the problem is that extreme specialisation is almost always extreme vested interest. Moreover, those who productively rock boats are rarely those on-board, and extreme specialisation means no-one is qualified to make waves except those with the most to lose.