Both deformity and beauty have been used for antagonists so many times that you can't really help but have a cliche.
If you have the extremes of beautiful, ugly, and normal, and villains have fallen into all three categories, you can't call ANY of them cliché , because you run out of options. Trees that grow without green on them in the villain's chosen land is a cliché, oh, unless his land happens to have suffered from severe droughts so that the trees can't get the water they need. We see things as being cliché whether they are or not because so many things have been done so many times. You run out of "new" options the second you start dismissing the old ones.
That aside, Voldemort wasn't disfigured because he was evil and it was effective, he was disfigured due to the process by which he maintained his immortality, the process by which he regained a body, and his connection to serpents. J.K. Rowling had a clear idea as to what he looked like in his various states and why. She even made it clear that prior to his first death, he was an extremely attractive, talented young man, so you can't really say that he is an example of a disfigured villain when he crosses into both of your categories over the course of the whole tale. That's what adds depth. He's not a monster in the sense that he's born of some unnatural creature (okay, that could be argued, but at least the woman was still technically human), it's his decisions, actions, and methods that lead us to
realize him as the monster he is.
So I'm not sure what more could be said on the matter, since I agree that it is really about what you see his motivations, lifestyle, and disposition to be. Before you decide what he is, give him a chance to tell you WHO he is. Make up scenes for him to live in and see what he does, what he wears, how he speaks. It might really clear things up for you.