OK, a couple of points to clarify...
- How your bike is remapped depends on the product you choose. For example, Yoshimura has a box that changes the stored program in your bike's ECU (engine control unit). Once you make the change, you remove the tool. Factory Tuning also has a similar method. Other options such as the Power Commander and Yosh EMS are a piggy-back system where the bike's ECU maintains its original programming and you install and additional box in-line with the ECU to modify the signal sent to certain components. In most cases that is just the fuel injectors and sometimes ignition timing.
- These piggy-back modules typically modify the amount of time the fuel injector is held open each time it pulses (also known as injector duty cycle or IDC) as a percentage of what the factory ECU is calling for at a given RPM and throttle position. For example, at 10,000 rpm and 80%TP your bike might need 10% more fuel than what the stock ECU programming is calling for so you program this module to make that adjustment.
- The manufacturer's do tend to program their ECU's (or set idle circuits on carbs) on the lean side at idle to help meet emissions requirements. They also tend to set them a bit rich at WOT to help prevent the damage that comes with running too lean too long. Also, no two bikes are exactly identical due to production tolerances therefore they are set according to averages. This is why even a stock bike can benefit from rejetting or remapping.
I'm sure there is more to say, but it's getting late and I need to head off soon. Feel free to post any other questions.
Rarely is the question stupid, but sometimes the answer is
you need to run everything you read online through your own personal BS meter to determine if it makes sense to you.