you can create a folder named "RepositoryTemplates" in a "Portals/#" folder, then copy a template from the DesktopModules location. The module always looks in the current portal folder first, then the DesktopModule folder second.
so..for example, to have different articles templates for each portal...
/DesktopModules/Repository/Templates/articles/... ( global to all portals )
/Portals/0/RepositoryTemplates/articles/... ( for portal 0 only )
/Portals/1/RepositoryTemplates/... ( since no articles template, portal 1 will use the template in DesktopModules )
/Portals/2/RepositoryTemplates/articles/... ( for portal 2 only )