I think some rules don't make sense, and others don't address problems correctly. I see personally that if you jump for the ball, you leave yourself open to injury from other players jumping at you "going for the ball". So defending yourself by raising your legs is smart, plus it can help you get more air (how Michael Jordan used to jump so high and maintain so much air time). Your basketball analogy doesn't really work, as that sort of contact is blatant and not a part of the game. But in soccer, jumping for the ball, slide tackling, and clipping are common occurrences while going for the ball.

Some of what Pepe does is obviously foul and violent, like kicking that first guy repeatedly in the video. Dirty is more subjective, as you said, it skirts the line of what's allowed and what's not.