Most users don't need to know about SS, SCK, MOSI, and MISO. I set SS to output and set it high in init(). That makes SdFat work with boards that don't use SS as chip select for the SD. If another SPI device uses SS as chip select this disables it.
The only time you need to worry about another SPI devices is if it uses a pin other than SS for chip select. You must set chip select high on that device before calling SdFat::init().
I don't want users to edit Sd2PinMap.h It is generated by a program that I run.
You are an exception since you are making your own board. You will always need to edit Sd2PinMap.h since the 1284P is defined to be a Sanguino in Sd2PinMap.h.
Early versions of SdFat had SD_CHIP_SELECT_PIN in the same file as SS_PIN, SCK_PIN, MOSI_PIN, and MISO_PIN. Users thought they could change the pin numbers any way they wanted. That caused a lot of problems.
I wish I could remove the definition for SD_CHIP_SELECT_PIN and require users to call
sd.init(SPI_FULL_SPEED, chipSelect);
if chip select is not SS.
I plan to move the definition of SD_CHIP_SELECT_PIN to SdFatConfig.h and have a policy that users should only edit SdFatConfig.h.