What makes a common flaw (relatively) unique is how the protagonist deals with (or avoids dealing with) it.

Say the protagonist’s wife is dead. The husband can be in a state of denial, refusing to move on. Or he can feel responsible and be afraid of hurting someone else. Or he can secretly feel relief but not admit that to himself, choosing instead to phony, exaggerated grieving. The number of coping strategies is greater than the number of possible flaws.

Unless the protagonist is actively involved in fixing the flaw (or seeking unity), her or his coping strategy is not likely to elicit sympathy / empathy from the audience but understanding (or if the reason for the maladaptive behavior isn’t clear, it can elicit curiosity). (Technically the death of the wife isn’t in itself a flaw of character — it can be a source of pain, and we do tend to feel sympathy or empathy for people in pain, but still that’s pretty limited as an emotional response from the audience — “Oh, how sad.”) Once the audience sees that the coping strategy is itself a character flaw, they can root for the protagonist to abandon the failed coping mechanism just as strongly as the audience wants the protagonist to achieve the outer goal (and of course the two levels are usually interdependent).

As you point out, the writer should avoid outside-in strategies when introducing flaws. Often (in my case at least), what I had identified as the flaw (via conscious, left-brain thinking) changes during the revising process, as I hone in on a truer and deeper insight. As you’ve also pointed out, Scott, you have to listen to your characters.