The first step after reading in the stick values is to take whatever the range is and convert it to [-1.0,+1.0]. That is what the transmitter wizard calibration is all about, so it doesn't matter how you set your transmitter; so it is best to just set your transmitter up with stock settings.
ESC calibration on the output does the same thing. Throttle is handled a little differently. Anything negative makes it output the min. Zero makes it put out neutral (motors idling). Positive is the actual range used.
There are many things that go on in between. Your throttle stick may be in the middle, and the average motor may be doing 50% output, but each individual motor gets moved up or down from 50% according to what the stabilization wants.