As I said no need to rehash things already posted in this very thread. Feel free to read through the thread again for details. But just a couple new points.
The ECU is limited to the logic path that is provided by the operating system. With flash tuning you're generally able to modify existing tables with new values, but you are not generally able to recreate new logic paths or dramatically change paths that are disadvantageous to performance. If you start to study flash tuned logs you'll find that in many cases the ECU doesn't abort runs when you expect it would. For example it allows full boost at a super lean 18:1 AFR and fuel pressure on the verge of collapse. Meanwhile with the JB4 you have whatever safety the ECU/flash offers PLUS have an intelligent programmable system looking at vehicle data full time all the time able to layer in extra logic.
Most flash tuners sell non-integrated piggybacks under different names to make up for the ECU's operational shortcomings. They are known as external water/meth controllers, external fuel pump controllers, 2STEP/WOT box, electronic boost controllers (in the case of Lap3's turbo kit), logging dongles, hobbs switches, etc, etc. These non-integrated systems are required to make up for shortcomings of the ECU but since the can't all communicate with each other are inherently less effective and safe than one external system like the JB4 that can do everything you need.