When Maya loads environment variable settings into its memory, it adds some standard paths to certain environment variables to ensure that some things Maya requires to run are always available. This affects the following variables:
MAYA_PLUG_IN_PATH MAYA_MODULE_PATH MAYA_SCRIPT_PATH XBMLANGPATH
When you set these paths yourself, variables you set using the operating system methods override all other settings, variables you set in Maya.env override standard settings, and the standard settings are used if not overridden by system variables or Maya.env.
Because your path settings take priority over standard Maya paths, it is possible to override files which Maya needs to run if one of the directories in your path settings contains a file of the same name. Care should be taken to avoid this as it may lead to Maya failing to execute properly.
On Windows and Linux, you can try starting Maya with only default settings by typing maya -default at the command line.
For the system PATH variable, Maya adds $MAYA_LOCATION/bin. On Linux, it also adds /usr/autodesk/com/bin.
Maya checks whether the directory specified by the HOME variable (Linux, Mac OS X) or USERPROFILE variable (Windows) exists and is writable. If not, Maya issues a prompt for you to provide a writable home directory. Note that HOME and USERPROFILE cannot be set in the Maya.env file.