Stock for stock it's extremely close with the RT holding a slight advantage. And by slight I mean one, maybe two tenths. People have pulled 13.3 on a stock mustang if you know where to look. Typical? Ofcourse not. But then neither is 13.1 in an RT.
Regarding what's a "fair" comparison or not haven't we all seen this huge gray area argued a million times over? Considering you can get a brand new mustang GT out the door for 22-24K right now perhaps we should compare it to the Challenger SE?
All depends on how you want to go about drawing comparisons as far as who "wins" or not. It's debatable what is the most fair way to go about these things.