In all cases, after correctly / successfully running the wizard / transmitter-wizard and saving the result, you should not touch the input reversing.
For a multicopter, both the input and output reversing is automatically set correctly if you use the wizard / transmitter-wizard. (The only possible issue (I have never seen it) is for your ESC throttles to be designed backwards and that would require you to reverse all motor outputs.)
For an airplane, only the input reversing is automatically set correctly when you use the wizard / transmitter-wizard. It is up to the builder to get control surface direction and throttle correct by reversing ONLY THE OUTPUTS for airplanes.
If you incorrectly reverse the outputs (or leave them in the incorrect direction and think that reversing the inputs will fix it) then the stabilization is backwards, so instead of seeing that it is banked left and commanding a right to straighten it out, it is commanding a left and it gets worse. This happens in the blink of an eye and the aircraft flips faster and faster and faster until it crashes.
Of course this only is a problem for the 4 stabilized channels. The others can be changed at will.
Two wrongs (reversings on input and output) DO NOT make a right. This works in manual mode when the reversed inputs are immediately reversed again by the outputs, but when the FC is stabilizing, it's inputs are not reversed, but the outputs are reversed and you get instant flips till it crashes.