I've noticed that the R/Ts tend to have better 60' times than SRTs. That is most likely due to Variable Valve Timing. If you can get out of the hole well, the rest of the run follows. So with a few mild upgrades, an R/T can be equal to an SRT at the track. But if you look at the incrementals, the cars get the 1/4 mile times in different ways. Even though the two cars are mostly the same, how the engine is setup makes a big difference.
Of course the 2011 SRTs have VVT now, and that's the biggest improvement with those cars. Making a 2011 R/T run like a 2011 SRT is a much bigger chore. A bone stock (w/video evidence) 2011 Challenger SRT 392 ran 12.44 at Infineon Raceway (Sonoma, CA) at 110 MPH with the notorious head winds there, and the driver didn't know what he was doing. My 2009 SRT, with a bunch of (mild) upgrades doesn't even come close. Stock I ran 13.6 and now I run 12.7. Still a long way from 2011 numbers.
So getting an R/T to run like an SRT is a complicated issue. Of course, if you want to beat a stock SRT with ease, nitrous oxide is simple and a blower works well also.
[alfred10, if you mean to ask why some stock R/Ts seem to get better times than stock SRTs, it because of all the other variables besides the cars. No two tracks are the same, no two drivers are the same, and even no two cars are the same. Some R/Ts came with better engines than others by luck of the draw and the same goes with SRTs. Also, the variances in the weather makes a huge difference. With my car, on a hot day I'll run 13.2s and on a cold day I'll run 12.7s, with no other changes. Hope all this answers your question.]