I am not aware of "primary" nominee being an official/legal term in the nomination process, only "Principal." I think it's logical that the words, being so similar in spelling and meaning, would used interchangeably by a MOC staffer. I don't think they are denoting two different classes of nominees when saying Primary vs Principal.
Based on my (parent) experience in this process, I think there is an error on the MOC end.
Either
1) They don't understand what they are saying/writing to candidates when they confer that the candidates are principal/primary nominees;
2) There is a disconnect between the members of the screening committee, which likely makes the "Principal" determination maybe on a weekend after some interviews, and the office staffer who comes in on Monday and actually submits the slate to USNA, e.g. somebody forgot to tell someone that one of the 10 candidates was a principal nominee;
3) Operator error by the MOC office staffer when submitting the slate. For example, he/she logs into USNA system to submit slate and sees a nomination slate menu and picks "competitive" (instead of Principal and Unranked/Ranked) and then lists the ten names in ranked order thinking that placing one name at the top of a list of 10 is the same thing as actually checking a box beside a name to denote Principal.
Staffers come and go and there are 535 of them vs one USNA admissions office with all the QC that the military is known for. I bet the training at USNA's end is better than the training on the MOC end.
Hanlon's razor - never attribute to malice that which is adequately explained by stupidity.