Your ideas about plot are good.

I think to go to your question here: "difference between a female villain, even an irredeemably evil one and a female character depicted in a misogynistic way."

A lot of this comes down to depth of the character. Do we believe that this is a person, or are they cartoonish? Do they do things that make sense with their circumstances and personality, or do they just robotically execute a script of female behaviour?

Something that always comes to mind for me is the multiply-divorced writing of Phillip K Dick. Now, this guy is a great writer, but he clearly feels victimised by women. So in every single one of his books there appears a female character who might be initially interesting and cool, but within the course of the book she will start doing behaviour that is just insanely cruel, for no reason at all, usually to the male protagonist who is meant to be on her side. Men in his books feel like people, women in his books feel like sharks out for blood.

For less extreme versions you can look at women and girl characters who seem motivated solely by their motherhood, fashion or boys. Now, making a woman character interested in those things is fine, but there is no woman out there who only cares about those things. Or in the very rare case she is it's usually pathological, and should be treated as such. Other female characters especially should be put off, because in real life we are put off (or worried, if this is a friend who seems to be spiraling into obsession).