I sometimes feel like people over think the logic of stories that are meant to be fiction.
Heck, you can set up a character buying a new sports bra then have the twist being that it ends up being bullet proof. Yeah it’s silly and not 100% realistic. But that’s the whole concept of suspension of disbelief. As long as you have the set up and pay off, most readers won’t care. Similar to how the Christian preacher gets saved by the Bible in his pocket blocking the bullet.
As for the villain, I think some people will fire their gun when they are stressed or frustrated. If the protag is doing something the villain doesn’t want them to do, that could be a reason for them to shoot.