Since Bungie has started mentioning all kinds of goodies about Halo Reach they have mentioned that the customizations you make will show in all areas of the game including the cut scenes. Here is proof straight from Bungie's Website with a character that they had modded during a reveal.
and then showing off Bungies sense of humor a little up-skirt Spartan style..
Extended version of campaign level from E3...
Tip of the Spear Preview:

