Analog PMUX settings...

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It seems that PMUX setting B ("analog functionality") of SAMDxx (I'm looking at SAMD51, specifically) has  up to 7 different functions associated with it, and some pins can do 5 of them:

 

PA02 ADC0 AIN0 pmuxB
PA03 ADC0 AIN1 pmuxB
PA03 ADC0 X0 pmuxB
PA03 ADC0 Y0 pmuxB
PA03 ADC0 VREFA pmuxB

 

What controls which one is "active" ?

 

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The active pins are the ones configured in the peripherals. You avoid conflicts by selecting what the pin is used for and activate only that function in a peripheral. Example: you connect a reference voltage on PA03 for ADC0, now you can't use that pin as AIN1. It can also not be used for peripheral touch control.

/Lars