Why ask when you seem to have already made the decision? ;D
I'm guessing when I say this, but I bet all the software upgrades are pretty similar.
As a programmer that deals with reverse engineering, I'm sure the engine control has paramaters, the software just changes those parameters. Dirt simple. The process to get the most power is probably somthing like; make a change, run a dyno, make a change, run a dyno, make a change, run a dyno, make a change run a dyno, ooops, we blew the engine, take out that change and try a different one, run a dyno, and so on and so forth. I'm sure that they make very educated decisions on what parameters to change. They might even write software that dynamicly changes the parameters in real time based on sensor feedback.
Bottom line, I'd bet all the tuners put thier best minds on it, follow a similar process, and probably end up with a similar results.
That being said, I'd reccomend picking a tuner based on thier reputation for standing behind thier work, not advertised dyno numbers. Either way, your fast will go faster
Hope that helps.