I apologize for it taking so long to get to this thread.
I had to actually read the notes to the left of the page to know what it was you were referring to. I have been set in my ways since the first Ikon (which is a bad thing!) and I just kind of breezed right through it.
So to answer your question, let me first post the question (or statement as it is in the manual).
Ikon Step 12 said:
1.) With blades removed or with the motor disengaged from the main gear, drop the MIN endpoint to ensure the system arms with the TX at zero throttle, then increase it slowly until the motor begins to spin, then back off 3-5 points
2.) Raise the throttle on the TX to 100% and slowly increase the MAX endpoint value until there is no longer any further increase in the motors RPM visible in the "Current main rotor" field at the bottom of this page. On some ESC, when the maximum output is reached, the on board LED will turn off
What they are wanting you to do is manually set the endpoints that you are adjusting to suit the ESC. I do this a little differently. In my case, I set everything where it is at 0 and 100 on the slider (or -100 to 100 on some) that way I know the Ikon is seeing full throws. Once that is done, if I need to do it, I will manually calibrate the ESC through the ESC itself to set the endpoints. This makes 100% sure you are getting absolute min and max out of the ESC.
One caveat though is that I do this on step 5 of the setup process. The only thing I do in step 12 is set my rpm's for the governor if I'm going to use it. Otherwise I just leave everything in that menu alone. The throttle in menu 5 is going to be the same as in menu 12 and by adjusting menu 12 (I'm assuming here as I have not actually tried this, but it makes sense lol), if you change the high and low points in menu 12, you are going to throw off menu 5. I wish I had time to actually test this, and I WILL be testing this in the future when I do have time, I just don't have a lot of it at this very moment.
I do hope this helps explain why I didn't follow their exact procedure. I just find manually calibrating the ESC to the controller is faster and more accurate (and safer) than the way they do it.