Just read the profiling manual. It talks about the process in there.
I have done just that. And in doing so I was actually surprised to see both of these statements.
"Since the Profiler sends its own test-tones into the reference amp during Profiling, it should be obvious that the sound of your guitar isn’t part of the result. The Profiler is designed to react to any guitar in an identical way to the reference amp that was profiled"
"The refining process is actually independent of the type of your guitar. It is about adapting the distortion characteristics, as well as polishing the attack and dynamic response. The resulting Profile will act and respond accurately no matter what guitar or pickup you use."
This has led me to believe that Keith Merrow as well as many other users of the kemper have not read the manual either.