What he's saying is that Justin will analyze your engines running condition (log file), and let you know if you have any sensors out of normal range causing performance loss. A code reader won't do that.
A shelf tuner will dump the same parameters on a stock truck, as it will on a truck with a cam, higher compression, and head work.
Justin will tune to match what your engine needs specifically. He'll also retune when you make changes, so you get the most out of your upgrade purchases.
There's really no comparison. You're not going to find anyone that says there's anything as good as a custom tune.....except maybe a hypertech salesman.