One 2001 GSXR750, had a milled head, thin base and head gaskets, degreed cams, BMC filter, and it had 12 horsepower less than a bone stock one I did the day before. I have had two that actually had less horsepower than they did stock. I have had many, many bikes brought to me after visiting a shop that used the autotune system and I always made them run better. Three same bikes basically all the same, with different exhaust systems will need three different maps to perform to their best possible state.
Now if all you want is a map that comes close then maybe a flash will suffice, but having spent hours on one racebike to get the best performance, I know that if I took that map and put it on another same year model it may not work as well. In my world, working with every version of Power Commander ever made, including the Fuel Nanny (bet you don't know what that is), the thing that I know holds true is that for peak performance no one map fits every like model! If I have three GSXR 750's to remap, I can guarantee you that all three will end up having different parameters. How do they know what the ECM needs for peak performance? Having spent years tuning bikes on my Dynojet dyno since before fuel injection and then into the fuel injection world, a question immediately arises in my mind. From what I gather, you send your ECM to somebody reliable, and they change the fuel injection parameters. Yes, I know what flashing means, but I'm unsure how and why it is done.