You shouldn't have to comment anything out. Don't use VisualStudio, use ArduinoIDE. It works better, IMHO. As was previously mentioned, make sure SdFat is version 1.1. Also, make the changes in
C:\Users\
yourusername\AppData\Local\Arduino15\packages\arduino\hardware\sam\1.6.12\platform.txt
In lines 22, 24 and 28, change one of the parameters to read:
-O3
The -O3 will give you a big boost in speed.
With nothing commented out and all my preferred options set in config.h and host_due.h, I get this output form a test compile:
Sketch uses 506244 bytes (96%) of program storage space. Maximum is 524288 bytes.