So as someone who is writing a villainous type protagonist for my comic, I'll try and share my perspective. (Not that I'm super qualified or anything! )
So you mention these 4 ways that you think a villain could be the main character, and number 2 really stood out to me because it was the only one that didn't rely on comedy or misunderstanding. But it's also the "weakest" one you mentioned when it really doesn't have to be.
Here's the issue:
Why does the villain have to justify and explain constantly?
Does it make sense for the character or is it just to prove something to the reader?
Because if you want to prove to the reader why your protagonist is doing evil things, it's much more compelling to show those things directly to them. It doesn't have to be perfect reasoning, just understandable. And if a character thinks they are doing the right thing, show that through actions instead of just repeating dialogue. A character with a stronger sense of righteousness will actually spend less time explaining because to them there is nothing to explain. Also, it's best to avoid too much angsty dialogue at once lol.
A good character just needs a good motivation. If you can just give your protagonist that, it doesn't matter if they are good or evil. Then you just have to show the struggles to fulfill that motivation (aka conflict).
Most of the best villains are compelling. They have a sense of charisma even if they aren't people-oriented. They have to have at least some attractive qualities for the reader to want to continue the story. No person is purely black or white morally. Just like a hero has flaws, a villain will have virtues.
And how do you end their story? Well you can have them fail in a justified way, or maybe they succeed and you see how the world is affected by that.
Even if the protagonist is evil, most readers will kind of root for them anyway since that's what stories train us to do. So don't be afraid to think that's an option!
Overall, writing a villain is a lot harder than a hero protagonist but it's not impossible. Other people in this thread gave great examples that are worth checking out! And not everyone will enjoy the character, but that's true of every character and story.
Hope you get some answers that help! I think writing villains is really fun so it's worth the effort.