Take a look at the flash programming hardware (under the Nios II kit install/comonents/<name of your board>) From there you can see what the flash programmer sends to the board first before programming the flash (need to have a hardware design present to do the flash programming). If you have to modify that hardware be sure to backup the original (just in case you break it). Also the contents are read only so you would have to change that as well.
My question is are you going after higher access speeds to flash (usually most people don't care too much about flash access speed and just use it in 8/16 bit modes).