It is also important to understand that the reason these things are often conflated is that much of what is (or at least used to be before quantum computation became a thing) taught as quantum mechanics focuses on the special case of a single particle considered in isolation. In that one special case -- and ONLY in that one special case -- configuration space is the same as (or at least isomorphic to) physical space. But as soon as you add a second particle, that stops being true.
So the key to understanding QM is to START with the multi-particle case. This is actually easier than the single particle case because it forces you to set aside a lot of the things that make quantum mechanics difficult in general and focus on the thing that makes it hard to wrap your brain around: entanglement. But the reason that entanglement is hard to wrap your brain around is that it's weird when considered from the point of view of physical space. If you start with multi-particle systems, that forces you to start with configuration space, and that gets you past the hard part right from the start. After that it's just math.