Historically, simplifying a great deal and looking at tendencies while skipping major figures, I think that Descartes invoked God as an assurance that we can't obviously be mistaken about our common beliefs. Though we can't explain mind, we can say a great deal about bodes.
Along comes Locke and says, we can't go that far, yes, ultimately, we are in the hands of the Almighty for ultimate causes, because we just don't understand them.
But already there are seeds that, by merely looking at ordinary objects, we have trouble, we can't really say if secondary qualities exist in the objects or not, but it doesn't matter for our practical affairs. Nor do we know essences - if they even exist.
Then Hume comes along and says, all we have empirical verifiable evidence for is constant conjunction, but this does not mean that's all there is to causality, it's merely what we can say with confidence about it.
Many things, including experiencing one object being the same after two different instances of perception are a "fiction" - his word - meaning, more than can be empirically verified, but a sensible postulate. Along with this, he points out that our individuating objects as one being different from another, is another fiction, useful, but not at all certain.
Beyond that, going through Kant and beyond, the project seems to me to simultaneously show how little we can say confidently about the world, while sticking to causal relations, connected by us and
assumed to belong to the world - and we've had great success.
But as each major figure advances, the key is, as you say, being utterly baffled by what we assume to be true and realizing, after close scrutiny, that our common sense beliefs do not hold up to the mind-independent world. I think the case is both, our understanding is in fact incomplete and we have to catch ourselves from sweeping things under the rug. Today we hear people say "that
obviously follows from learning/natural selection/laws of physics".
The problem here, is that the gap between physics and biology to the psychology of a human being, in terms of complexity, is just massive.