I agree that there's a core misunderstanding here.
Villainess comics are usually do not think the protagonist is/should be a villain, they're often exploring what media and society drama as a villain. The catharsis is not "haha I'm evil, I can do whatever I want", it's "I tried to meet up to society's expectations until it broke me, and I was still made into the bad guy in the story, so now I'm going to stop worrying about what everyone else wants and live my life, even if that's seen as evil"
Villainess characters are usually characters who tried to be 'good', but did it 'wrong'. They were naïve and spoiled, so were easy to frame, and now plan to be smart and ruthless. They were smart and competent, and were seen as cold and unlikable, so are now pretending to be cute and sweet while manipulating everyone. They spent their life trying to keep everyone happy, and got thrown under the bus, so now they're going to live freely.
As I mentioned in my post, you've got to remember the major audience of this is young Korean women who are coming of age in a society where there is huge pressure to be competitive and academic, but also huge pressure to be sweet and feminine. I think the stories are meant to resonate with girls who grew up being told that, if they lived The Right Way, they'd have a good life, and are now being punished for being that. They focused on academics, and now they're seen as cold and ugly and unmarriageable. They focused on relationships and now they're seen as shallow and slutty. (in fact, lots of modern to historical Isekai will explicitly reference modern Korean issues like men having affairs being seen as a failure of their wife to keep them happy, or sons being favored and seen as having 'more of a future')
A lot of villainess characters are contrasted with the girl who did it 'right', who is loved and accepted and seen as pure yet sexy, emotional yet calm, hard working yet relaxed. Some of these characters are the story's actual antagonist, some become friends. In my favorite stories, they are sympathic characters crumbling to meet the impossible standards the 'villainess' failed.
tldr: 'Villainess' here does not mean 'evil', it means 'social pariah, somebody who society sees as a villainess'