The variables set in the operating system take priority over any settings in the Maya.env file. However, when Maya verifies the environment settings, it may add default settings.
On Linux and macOS, you can use export on the command line to set environment variables. You can add commands to your .bashrc file to make sure the environment variables are always available.
export MAYA_SCRIPT_PATH=/remote/scriptDisk/scriptFiles/
set MAYA_SCRIPT_PATH=/remote/scriptDisk/scriptFiles/