The Freescale compiler is an ARM compiler made by Freescale and only supports the M4, but not the M0.
The GNU compiler is from ARM Inc, and supports the M4 and M0. Of course as they are different compilers, the options are different.
If you want to move over a project from one to another. I recommend that you create a new project with the wizard (File > New (Bareboard) Project) and then add your source files.
Hope this helps.