1. Don't worry about it too much. Just write what you want to write first and foremost.

2.
>is a male hero that battles a female villain a triumph of the patriarchy?
No. Any feminist pop-culture critic worth his or her salt understands that an inclusive work doesn't automatically have to have women in "good" roles; it means the work includes female characters that are just as nuanced and unique as the male characters. ie: the women can be heroes and villains, likeable and unlikeable, rich and poor, ugly and attractive, etc etc etc. Your work is only non-inclusive/antifeminist/sexist if the female characters are only important relative to the male characters or only exist as stereotypes next to fleshed out male characters.

If you write a story where there is a male hero and a male villain and the only female characters in the story are the hero's love interest and maybe the villains femme fatale sidekick, you're going to fail the Bechdel Test. If you write a story where there is a male hero and a female villain, as you propose in your post, there is nothing inherently sexist or antifeminist about that work and anyone who says otherwise is reaching. Unless of course your villain is a sexist stereotype of some kind, in which case you not only fail the Bechdel Test but are also probably a lazy writer for having a major character of any gender who is a narrow stereotype..

So yeah, don't worry about it too much. If you write a story that just happens to have an all-male cast, you're not a bad person.

In conclusion: don't overthink it to appease some invisible critics. Writing to please invisible critics is never a way to go. And when you do write female characters, put the same care and attention into them as you do your male characters. Problem solved