I think you can trust your feelings about the story itself – not just the storytelling, but also your feelings about what’s driving the characters, what their situations are etc. Underneath those things lies, in my experience, a structure, or set of potential structures.
But you’re right that you can’t necessarily trust your feelings about Dramatica elements; that involves a tricky kind of translation between different parts of your mind. (This is where getting more experience with Dramatica, both writing and analysing, really helps – you get a feel for the elements.)