The modified Sd2PinMap.h for your board should work with this version of SdFat.
In the future Sd2PinMap.h will only be needed for software SPI.
Hardware SPI will be setup using just the avr port/bit for SPI. For example PB7 is SCK on your ATmega1284.
I only need the processor ID to setup SS, MOSI, MISO, and SCK.
The Arduino files will only be used for chip select.
I will also produce a version of SdFat that runs without any Arduino core stuff, just what comes with WinAVR.
In the Arduino free version, chip select will be specified by port/bit like this:
if (!sd.init("D3")) sd.initErrorHalt();
Assuming chip select is connected to PD3.