It is unlikely that SdFat will support 4-bit SDIO on SAM3X since it won't work on Due.
I am reconsidering support for non Arduino boards. I can't test unless I have a board and it's a lot of labor for a few users.
I have been playing with SDIO on STM32F4 for my own RTOS use. SDIO provides super performance but you need large transfers with a lot of buffer.
I would be interested to know what Arduino applications would require more than a few MB/sec of I/O to an SD card.