Altera Monitor Program nios2-elf-gcc compiler flags

I'm not sure what the "Altera Monitor Program" is but to answer the question yes those flags can edited.

If the software is compiled from the command line chances are it is done through a shell script. Open the script and look for those flags and remove the ones you don't need.

If the software is compiled from the Nios II software build tools for Eclipse then right click the project and go into the options/properties and you should be able to find those flags being set (just remove them).

Ok now that being said if the mno-cache-volatile flag was being set then the application code might have been written to rely on that flag being present. What this means is that if you remove that flag you might need to modify the application so that instead of relying on volatile pointers accessing peripherals that those locations either be mapped to non-cacheable pointers or accessed via IOWR/IORD macros. You could also install the legacy Nios II tools (installed by default if you use the unified installer in 11.0) which comes with the gcc3 toolchain.