It really makes no difference tbh.
He defends almost as much as he attacks, he attacks as much as he defends.
Rafael is always getting up and down the pitch, they work as a team unit rather than a "winger and defender".
Just because he starts in the rb position would not mean he is strictly a defender, just means he will be marking the left winger rather than the fullback.
It suits him quite well infact, he likes to stick wide and play his way into position, rather than dodge and dribble passed 3 players. Leaving him wide would allow Nani to move around and come inside infront of him.
Valencia is more than good enough to do a job at RB.
Know where you're coming from, but it does make a difference. Valencia at right-back is still capable of going down the line but he is slightly more limited since his starting position is deeper. Even he can sometimes tire I believe, and it's no good loosing even ounce of his energy. Against Chelsea at Stamford he still made 2 or 3 good, winger runs but that was about it. It will be easier for big teams to stop him from there.
Apart from that, I'm sick of playing our best players out of position. Most of them have suffered from it in my opinion. Club like Manchester United can't enter the season without a proper, genuine right-back.
And yes, Valencia is whole lot more than good enough to play as a full-back, he is too brilliant a winger to be sacrificed, though.
EDIT: I've been saying for a while now that Valencia's dream position would be wing-back. He would have been rated even higher 30 or 40 years ago I'm sure.