Hello @p_a_u_darshana
Yes, you can use the GCC 4.9 version with our toolbox. I cannot provide a list with limitations because it has been only tested with the GCC 6.2, the one delivered with our toolbox.
If you need to customize the compiler flags, you can go to our Config Block and under Build Toolchain you can update the GCC flags.

To switch the compiler, you are right, you have to set an environmental variable "GCC_S32K_TOOL" with the value you have mentioned. If you add this variable in Windows' path, don't forget to restart MATLAB to make it aware of this change. To check the new compiler, you can type the following command in MATLAB's Command window: getenv('GCC_S32K_TOOL')
Hope this helps,
Marius