Atmel SAM E70 SPI Chip-Select (SPCS) lines
Being an output or an input has nothing to do with what your lines will do if they are configured as Chip selects.

You may either configure them as GPIOs (in which case they have nothing to do with the SPI subsystem) or as SPCS lines (in which case the GPIO configuration becomes irrelevant). Of course you are able to only configure 1 or 2 or 3 chip selects and the other line(s) as GPIOs (inputs or outputs).