Well, you're right. But our stock exhaust can easily handle an additional 50 or more horsepower. I have yet to see (and I don't know everything) a dyno or 1/4 mile test showing an increase in power over a stock exhaust with just an exhaust system mod. They always throw parts at them like the camshaft dyno tests.
We always made one change to our cars and then raced them at the track. Then made another and raced them again. This allowed us to quickly identify the stuff that was all hype and didn't work or just not needed as the factory parts were good enough for our purposes.
Now this is just my opinion, I think the only benefit you'll get from those shorty headers is more cabin noise and future exhaust leaks. Regardless, it would be best to add the supercharger and then test the truck. Now, you can download apps to your phone and have a portable drag strip if you can find a deserted road if a track is not close by. They are never convenient, but chasing power robbing culprits is worse.
I once drove up to Gainesville's drag strip to run some of our cars. There was this one Buick that looked like it would blow our doors off with all the stuff he had on it but after it's third pass, it as no faster than a showroom original. Seeing how mine was completely stock (appearing) and two seconds faster than his, he sought my counsel and we proceeded to pull parts off the car and it kept going faster and faster. By the end of the night I had him banging on the door of the 11s. One of the biggest performance gains was to un upgrade his fuel system. We bypassed the massive fuel lines and external Walboro fuel pump and adjustable FPR and wired up the stock fuel pump and lines and a got a spare stock FPR back on his car with a little tweaking and we were in business. Curiously, when I had the race shop, the biggest gains my customers saw was removing all the junk that they had been sold and just tweaking the factory parts.