Friends have told NBC News that Benedict was transgender and primarily went by he/him pronouns at school but also used they/them pronouns, which Benedict’s family also used. Several other friends said Benedict preferred he/him pronouns.
I don't really care what his mother called him, but the quote from the article seems to disagree with you
Look bud. I get that you want a trusty point of reference for their gender, and kudos to you on that. The whole reason they were brutally beaten to death is because of their gender non conformity. Them being trans has been the whole reason the police has been so virulent in their disinformation.
If you believe there is possible doubt about what they said their gender was or you are confused by conflicting sources, maybe just say Nex?