Customization of an Arduino library on Github

Do you mean this definition in Common.h?

typedef enum {
  INPUT           = 0x0,
  OUTPUT          = 0x1,
  INPUT_PULLUP    = 0x2,
  INPUT_PULLDOWN  = 0x3,
} PinMode;

That should not be used anywhere except when calling pinMode():
void pinMode( pin_size_t ulPin, PinMode ulMode )

You should be able to set those enumerated values to anything you like and when the core gets re-compiled it will use the new definitions. The code will behave exactly the same unless someone DOESN'T use the enum when calling pinMode().