These are normal pins with a header - the alternative fucntion is jsut on the back - so on the top they are labeled with the pin number on the back they are labeled "WIFI RTS" "WIFI CTS" etc.
The reason the pin numbers go higher than 99 is that we numbered them to avoid conflict with any pins that Arduino folks had already defined for the Due, and have our pin numbers be contiguous, as they used some pin numbers in the 70s and 80s range to assign to pins that aren't broken out but are useable - we've left these definitions in place as well, so some pins can be accessed by two numbers.