My experience with LS2 edit is that aftermarket tunes are always modifications of the basic factory tune. I have been told that there are many thousands of paramaters in a LOT of data tables that form the basis for the allowable states for each of the tuning decisions that the ECM makes. An after market tune must start with the same data and factory algorythms and modify them. Else you could never afford to buy a tune that has thousands of hours of engineering invested into it.
So the after market tunes modify some of the data in the tables and / or plays with the variables in the algorythms that command the various states in the motor in real time.
Part of the challenge is that most tunes are encoded in some form of machine language that is not interprable by humans without an extraordinary amount of work. Or by decrypting / translating them using a specialized tool.
So after market tuners spend time and energy figuring out what the current software is, guessing at what paramaters if changed will provide a changed (positive) result, and then generating those changes and testing them.
There is nothing magic about an after market tune. The magic is in knowing how to read the code and then knowing what to change to achieve a specific end result.
My personal belief, and one of the reasons that I chose to go with the LS conversion over bulking up my 2.0 is that while there is room for growth above the 260 ft pounds and even above the 340 ft pounds of torque, I have read many instances of motors failing once you get much above 350 ft pounds and ~400 HP. I was faced with the alternative of spending a few thousand on a motor that would never provide all the desired characteristics but would be a lot of fun, and that would probably shorten its life considerably. So I was looking at the probabability of spending a lot to get to the performance levels I wanted, potentially multiple times.
If anyone asked me, and they have not, I would recommend going with the GMPP tune, bolt on a high flow cat, enjoy a very good performing car that will most likely still give you 100k worry free miles. And which is backed by the GM engineering team vrs an after market tune that may or may not be fully supported in 3 years.