Several things are wrong with this argument. 1) This is a student athlete handbook as you can clearly see from the document headers. So it doesn’t apply to employees and what they are told to do.
2) These specific handbooks are written by someone within athletics and typically in the compliance office. It is in no way binding policy which would be handed down by the Title IX office and could be one of the reasons the Interim AD of that time frame was fired if there was at best a failure to update or at worst purposeful changing of their internal department policy.
3) You do not need to do the investigation to assess additional punishments. Typically the Title IX investigators will deliver a report to the supervisor or department head so they can take the appropriate action, usually with HR present.