Hello Rob,
I am deeply sorry for the delayed reply. We have been under a big workload.
Regarding your question, I understand the misunderstanding. Table 127 refers to input multiplexing which is different to the regular pin functionality that you are seeing in chapter 6. Please check the below description from UM.
The input multiplexer has no dedicated pins. However, several external pins can be selected as inputs to the SCT input multiplexer and all digital pins of ports 0 and 1 can be selected as inputs to the pin interrupts. Multiplexer inputs from external pins work independently of any function assigned to the pin through the switch matrix as long as no analog function is enabled.
If you refer to the table 95, you will see also that SCT0 input mux is connected to PIO0_2 though INPUT MUX.
I hope this helps!
Best regards,
Felipe
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