I don't think much changed in the EFI programming between '07 and '09 (excluding the TBW, natch). They've all been pretty good about accommodating, in a rather roundabout way, some freer-breathing parts. Not that I'd advise relying on it in any event. I know the '10s have some different programming, but all that I know of for sure about that is the fueling is now directly "lambda"-based with each cell allowing a range of values for closed-loop operation, the CLB tables have been done-away-with, and the VE tables are also "speed/density" now. Likely there are some refinements in the adaptive fueling, but maybe not.
If you put on freer mufflers, sure, you'll end up with the factory "lean" tune, but you'll also be making more power if you're moving more air because the proportionate amount of fuel will be added, too. Within the limits of the adaptive fueling window, of course.
So it's not quite the same as going to a dance as a wall-flower
