I know that charisma and physical appearance are two different things. But then again it's a well known psychological fact that beautiful people tend to have it easier in coversations and social interactions. At least during the initial interaction.
In the long run a charismatic but not so good looking character is going to win over a beautiful a-hole, especially when it comes to things as leadership, or just finding his place in a group that is forced together by unforeseen circumstances.
But as long as the beautiful person isn't completely inept at making coversation I thinkt hat he/she will have it easier to, lets say, convince a stranger he/she just met to tell him or her the latest rumours, or get the merchant to lower the price a bit on that piece of armor you're looking to buy.
And if you look like a troglodyte your 18 charisma is going to have a hard time compensating for that "first impression" thing. Strangers may turn away from you even before you get the chance to charm them with your silver tongue.
While I don't agree with OP's suggestion to have the charisma stat to impact your face options during character creation. Maybe it wouldn't be such a bad idea to add a stat for physical appearance as well and have that stat affect your interactions somewhat. (not going to happen, I know. But still).
And in a world where there are other intelligent being other than humans the phrase "beauty is in the eye of the beholder" is even more true. Who knows what a Beholder perceives as beatuy
And taking every race perceived notion of beauty in to account during interaction will be a not so easy undertaking.