Where to set the _USTN_WORKSETDGNWSTEMPLATE variable so it's not overwritten by the msconfig file

If I set the _USTN_WORKSETDGNWSTEMPLATE variable in a workspace config file, the msconfig.cfg is being looked at again (Specifically on line 471) and overwriting what I set at the workspace level. In doing so there is no way I can see to point to an alternative DGNWS file name for different workspaces.