"Coordination" is entirely up to the MOC, as is the policy of only nominating someone to one service academy. From my experience those seem to be general statements but not hard and fast rules. Who they nominate to which academy(ies) and the type of slate they submit, is entirely up to them and their team. It may even vary year to year. If they are especially impressed with a candidate for some reason, they may nominate that person to multiple academies even if their website indicates otherwise (I am aware of such a case in our local area last year; in contrast last year our congresswoman only nominated 9 to the USNA because she had a hard and fast rule about giving out multiple nominations).
Regardless of the lack of coordination, your son has two nominations: one from your congressman (I'm assuming that is a competitive nomination as you don't mention primary/alternate) and one from a senator (assuming that one is ranked and your DS is an alternate). Even though not the primary, that nomination still provides a mechanism for him to be appointed as he can compete on the National List, be selected if the primary gets disqualified medically or otherwise, or for a second senator slot if the senator seat has two vacant slots available this year.
Your son's friend also has two nominations, but the LOA implies that an offer of appointment is imminent (if fully qualified), with the the academy needing to decide how to charge his appointment: the congressman, senator, or the National List. If he is Primary for one of the slates, that decision has been simplified for them.
You don't state if your son and his friend have senatorial nominations from the same or different senators. If the same, it sounds like your son's friend is "primary" and your son is an alternate.