The domain part is hard coded into common/djangoapps/external_auth/views.py, so I'm inheriting that behavior here and it wouldn't matter as far as I can tell if you used a different cert domain.  For what it is worth, it appears to just be filler when using SSL auth, and is only used for CAS/Shibboleth. 

As for the other MIT specifics settings, I'm not really sure what to do.  The e-mail setting is probably easy to fix, but the one below with the long format string that determines an SSL username is tougher.  I can't imagine anyone using SSL right is going to want to add a user by typing in:
/C=US/ST=Massachusetts/O=Massachusetts Institute of Technology/OU=Client CA v1/CN=Carson Gee/emailAddress=cgee@MIT.EDU

to add a ssl user.  The other option is storing an unfilled format string in settings which seems bad, but maybe it isn't.  Would something like:
SSL_AUTH_EMAIL_DOMAIN = MIT.EDU
SSL_AUTH_CREDENTIAL_FORMAT_STRING = '/C=US/ST=Massachusetts/O=Massachusetts Institute of Technology/OU=Client CA v1/CN={0}/emailAddress={1}'
in settings be ok then?