Your using John Malkovich as a nominative example of the ugly archetype is interesting, if only in passing. Without consulting a filmography, I would assume that the full body of his work would indicate that the sizable majority of his roles have been of an obvious villain, or at least a character with clearly ambiguous motivations.
Although obviously my own aesthetic judgement, I don't find Malkovich ugly at all, but merely perhaps somewhat odd looking in his main features. I would say that he has utilized his physiognomy at times to accentuate some overt, extreme traits of certain characters, I think more to emphasize eccentricity than evil. But, overall I suspect that he simply finds the type of roles that have predominated in his career to be more stimulating and challenging. I would suggest that his association with them in the minds of the general audience is due to the superior quality of his acting chops, intuitive feel for a character's behavior and ability to incorporate expert physical movement in his repertoire rather than a fundamental, if unconscious perception of his appearance.
