The reality is that there are only modest gains to be realized in just retuning a stock system. The real gains are made tuning to specific mechanical changes eg. camshafts,

I'd be interested to know what these tuners are actually changing on stock engines. I suspect they are forcing the system into open loop ( like that which is available at Wide Open Throttle) and taking advantage of the A/F tables for that condition-open loop ( usually leaner). The problem with this is that it ignores any O2 Sensor control , which could have implications regarding it's ability to pass emissions tests and possibly could cause roasting of your cats.