A college or university can address sexual harassment affecting its students and others in any capacity it so chooses because this is specifically allowed under the Title IX Final Rule. Since the Title IX Final Rule went into effect, most schools, if not almost all, have specifically made policies that take this into account, where schools would be addressing Title IX specific allegations, harassment and misconduct that is, under their Title IX policies. They've also established separate policies, college or university sexual misconduct policies, that would cover, say, offenses that hadn't been previously covered under Title IX under these new policies that schools have since established.
In short, misconduct that was misconduct prior to the Title IX Final Rule in almost all instances will still be misconduct. It will depend on how the school will address the matter, but it's an important consideration to bear in mind. If 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.