Actually for this particular check, I think there may be a simple solution.

When AUTHENTICATION_BACKENDS is set only to the modelbackend (the default), consider a non-unique username-field to be an error, otherwise a warning that mentions your custom backend needs to handle this?

Also this entire comment thread is in the wrong place in this review ;-)
1) I commented on a test, instead of where the error is generated
2) this is for the check that USERNAME_FIELD is in REQUIRED_FIELDS

The check for uniqueness happens here:
https://github.com/django/django/pull/1364/files#L26R1062

and ....... uses Error level message