You can't assume that Howard assumed anything. They probably just thought her portfolio was interesting, and gave the scholarship on that. If you ask them they will likely tell you exactly that.
I can only go by what has been reported.
"Dolezal attended college in Mississippi, then went on to Howard University on scholarship -- not having identified herself black then on her application, because there was no such option, though people there may have assumed as much "because her portfolio of art was all African-American portraiture," her mother said."
http://www.cnn.com/2015/06/12/us/washington-spokane-naacp-rachel-dolezal-identity/