Radio calibration issues

I did the changes under the advanced parameters that changes the channel assignments so it coincided with my Specktrum/JR output scheme that I am ingrained in pretty well.

So the output is correct, i.e., channel one from the radio goes to channel one on the output side, etc down the line. Everything works the correct direction and such. All my travels at his point are 100% and everything is at default value in the transmitter.

When I use the MP radio calibration screen, none are right except the one that I did not change. So the one labeled throttle goes and does the input from the channel assigned to the APM module, a control surface. This is comin out all jumbled as I try to describe it. Everything works right but the MP shows wrong is the best way to put this.

Is this because I changed the channels and the MP does not change?

MP expects the predefined input and channel order. this has been like this forever. i would switch to the channel order used natively by the APM