designated spot. Running from gun gives RB a chance to quickly assess openings and then go. And in case it lends more credence to my argument, I played QB in HS and often called plays at the line in hurry up situations--our team found more success on short yardage with running from gun than under center--likely a function of having a RB with good vision.
I'm not saying one is inherently better, I'm just saying that I don't think one is inherently worse, especially if you know the strengths and weaknesses of your team.