Once upon a time, I thought wearing makeup made me look like less of a "real runner." Older and wiser, I now know there is no such thing as a real runner—anyone who runs is a real runner.
If you like the way you look with makeup on, wear some. I liked my race photos much more once I started wearing waterproof mascara, a little cream blush and tinted chapstick.
For guys who don't like how you look when you when you haven't shaved or trimmed your beard in a couple of days, wake up a bit earlier and groom yourself.
There are no rules when it comes to how you look in a race. If you prefer looking more like you do in your every day life, take the necessary steps to present yourself that way. If you're okay with the way you look naturally, then by all means, run as is—and be proud of it.