A college or university can address sexual harassment that affects its employees that fall outside of Title IX jurisdiction in any capacity the school chooses because this is specifically allowed under the Title IX Final Rule. Schools have done just that. They have their new Title IX policies per the Title IX Final Rule. They've also established a separate college or university sexual misconduct policy to address misconduct that is no longer covered under Title IX.
In short, misconduct that was misconduct prior to the Title IX Final Rule taking into effect will remain misconduct in almost all instances. It just would be addressed in a different capacity, say through the schools, college, or university sexual misconduct policy versus this Title IX policy. If you're a college or a university employee and you're facing a Title IX case, having an experienced attorney-advisor in your corner from as early as possible in the process will help you navigate the process and will help you work towards ensuring a fair process and a favorable outcome.