What people don't realize (I was one of them when I did the suitcase delete) is this isn't your 60s muscle car where you can stick the fattest pipe and biggest mufflers to get the best performance. The exhaust needs to be tuned to this car. I've personally seen the magnaflow system gain hp on the dyno.
Actually, I would argue its pretty much just like a 60's muscle car, which had a carb. and not fuel injection. You have to tune the engine just like the 60's engine to see the gain from the increase airflow. With the 60's muscle car, you would change the jets in the carb and take plug readings and even adjust the timing. With the Hemi, you will have to also adjust the fuel and possibly the timing as well, except you will use a computer to input a new fuel curve.
Remember, an engine is nothing but an airpump. The more air you can pump through it the more power you will make.
Because we have a speed density operating system, the Hemi is limited to its adjustments to increased airflow. It can't compensate like a Mass Airflow system can. If the magnaflow system is making more power than stock, yet a suitcase delete is making less than stock, then I would say the suitcase delete has increased the airflow rate beyond what the speed density system can handle and once tuned, ie. reprogrammed, it should yield a larger power increase than the magnaflow system.