Dreamer, I think you have the right idea and you make a very good point. The tune you were provided by Sam was for stock manifolds and cats. Adjusting the tune to include the long tubes will make up for some of that difference.
An example of a long tube header installation on a supercharged vehicle was a Kooks long tube header setup on a supercharged Saleen S281 Mustang. I have included the video below. After bolting on the headers, the installers retuned the vehicle to account for the new headers and made an additonal 40 rwhp and 35 lb-ft of torque.
RCZ, I'm not sure I agree with air flow being the killer of an engine. Your engine can be thought of as an air pump. In order to make gobs and gobs of power, you want to inhale and exhale as much as air as possible. This in turn means you can burn more fuel. This is where forced induction comes into play as turbocharger and supercharger kits will increase the mass flow rate of air into an engine. However, when picking a forced induction kit, you need to ask yourself one question; "at what PSI can I meet the required mass flow rate of air to reach my goal for XYZ rwhp?" More often than not, stock rotating assemblies will be the limiting factor in reaching your horsepower goals. The additional PSI will raise your peak cylinder pressures which not only means added compressive force on your pistons, but increased cylinder temperatures which leads to detonation.