Help with standalone SAM3X8E D4 and D10 pins

I've prototyped a device using the Arduino Due board, primarily doing cap sense work.
Now I'm working to create a standalone board for the actual product.

My questions are this...

D4 on the Due does not work as a cap sense input. Looking at the Due schematic I see D4 connects to pins 112 and 137 on the SAM3X8E processor.

Can anyone tell me why these two pins are connected together, and if it is necessary or not when wanting to use D4 as an input in a standalone setup?

I also see on the Due schematic, that D10 connects to pins 102 and 111. However I can still use D10 as a cap sense input without problem. Again, anyone know why these two pins are connected together on the SAM3X8E?

It does not appear that these processor pins for D4 output or D10 output go to anything other than those respective pin headers on the Due board.

The Due schematic also lists these pins as SS0 for pin 111, and SS1 for pin 112, but I'm unclear what SS"x" is. Anyone care to enlighten me?