System Identification PID Tuning: How do you let the PID Tuner know what parameters your step response output was performed under?

So I just read this article https://uk.mathworks.com/company/newsletters/articles/tuning-a-pid-controller-when-a-plant-model-is-not-available.html

And as useful and informative as it is, it left the question begging: How does the PID tuner know what conditions I executed my plant step response output under? In order for my system to output anything when there is a step input, one of my control gains (either P, I or D) needs to be set to a non-zero value. The PID tuner never asks for this to be inputted at any point.

Surely this means that the suggested control gains attained from tuning the system in the PID Tuner tool need to be applied ON TOP of the control gain applied for the input (when doing the system identification), essentially meaning the system is subject to two iterations of control. This makes no sense to me? Have I missed something?

****example and breakdown for those who don't fully understand the question:

I perform a step response of amplitude 10. My system has Kp of 50 for this example. I input the response of the system into the system identification tool and then load in the PID Tuner. I tune the PID response as desired. It gives me a value of Kp = 100. So a system with Kp = 50 needs to be subject to control of Kp =100 to give the response observed in the PID tuner. Is it as simple as adding the 50 to 100 when actually entering the values into my system?

[Pablo Martínez Cruz]

I have exactly the same question that you.

Did you find the answer to it?