Neither can USNA direct anything re the nomination process. They can recommend things that will help candidates but can't direct a civilian candidate to do anything.Especially when we know it was from a BGO volunteer who has not authority to direct anything in the process.
Just to be clear, USNA tells BGOs to advise their candidates to apply to all nom sources for which they're eligible. The BGO was likely passing along this advice. Whether it is a "direction" or "advice" lies in the tone and perception of those involved. It's up to the candidate whether to take the advice.
I agree that, for an LOA candidate with a Pres nom, it probably doesn't make sense to pursue MOC noms for that SA. However, for LOA candidates relying on MOC noms, nothing is set in stone until the slate is submitted to USNA, which could be as late as Jan. 31, regardless of when the candidate is notified of the nom by the MOC. I can envision all sorts of scenarios where the "original" nom falls through before it is submitted -- and I'm sure USNA has lived these scenarios.
Thus, they suggest everyone apply for all noms. If the MOCs don't want to duplicate noms for LOA (or other) candidates, they are certainly capable of getting together to ensure this doesn't happen -- and many do just that.