Hi @enricorocheti_
I hope you are doing great.
Currently, the SDK does not contain a sample .mex file showing most of the available pin configurations.
However, in regards to visualize available pins, the Pins tool lets you to see Arduino expansion header and create headers. That may be simpler to know which pin to choose on the EVK.

In regards to pin configuration, as you mention, if you want an example to know how configure a pin for a certain peripheral, the current way to get is to refer to the example that uses that peripheral.
All the best,
Diego