If the referee is contacted, their only job is to confirm your identity and that they've known you for at least 3 years. They aren't character references or anything, and they don't have to be friends; it could be a co-worker or boss from a past job, a neighbour, anyone really. I wouldn't risk having someone I didn't know in person. If you're really struggling, could you find a way of meeting your Skype friend in person before you apply?