There should be a WEM cfg repository (simply another git repo) that WEM can query. Users would be able to select configs from there to use for local setups, e.g.:
# Search for the cfg. If it's a first run scenario, clone down the
# cfg repo before trying to search.
wem search morrowind
# Maybe install isn't the right command for this, since it's
# already doing the actual app install..
wem install --cfg morrowind
The install part of the process would set various options based on the local setup.