I am in occasional contact with religious people, and they don't behave as the "separate magisteria" hypothesis would predict. [...] There is active denial here of something that belongs, in the magisterium of physical cause and effect, and active presumption of interference from the supposedly separate magisterium of faith.

Interactions between the magisteria are contradictions for you, not necessarily to a dualist who believes it all works out, somehow. (For example, somehow we know about the second magesterium, and knowledge of it has significance on our interaction with the first.)

Also complicating matters is that each religious person has their own location on a scale of self-consistency. I find that most religious people fall well short of self-consistent, but not as short as claiming the dragon doesn't breath just so the CO2 detector won't be used.

My point in the comments above is that when religious people claim that there is no evidence or counter-evidence for God, it's not as often a desperate measure to protect their belief, but simply that their belief in God is not meant to be about an empirical fact like a dragon would be.