First, you are assuming that the police failed to secure the apartment for hours after they notified Jones and made the arrests. That is something that none of us knows, but it's hard to imagine that the police would fail to secure a crime scene until they could get a search warrant to properly investigate. I'd be betting that teammates knew of the arrests before Jones ever got the call, and that the cops realized that teammates would consider cleaning things up given a chance. In fact, failure to secure would be potential grounds for dismissing a case - too much question regarding possibly removed, contaminated, or planted evidence; they don't want that kind of doubt cluttering up a case. Otherwise, why even bother with little niceties like chain of custody. And they aren't dumb enough to think that in this day and age that notifying a coach at any point in the process would go unnoticed - and the motive considered and hashed and rehashed - again and again - and then reviewed and reconsidered - again and again.
Second, you can pretty much bet that the local police will notify military or university or any other similar institution when they make an arrest. I made one of those typical student blunders a long time ago during my years at UT, and I can assure you that by the time I got back to campus there was a message from the Dean of Students waiting for me. I wasn't an athlete, but I can very definitely tell you that I did not have to inform him of my screw up so that he could place me on disciplinary probation. And for the record considering all the Title IX legal representation flap, he sent also sent me to discuss my situation with a lawyer in the College of Law.
IF you are correct when you assert, " I'd be betting that teammates knew of the arrests before Jones ever got the call, and that the cops realized that teammates would consider cleaning things up given a chance"
A few things are wrong, one, if teammates knew of the arrests, they should have called the coach, two, There shouldn't have been a thing to "Clean up". I hope, IF a rape took place, teammates wouldn't have involved themselves in a felony, after the fact, as a favor to their teammates. I hope you don't really believe our team is made up of guys, that given a chance would cover-up a rape, or help a rapist to escape justice, we're better than that.