"territory whose citizens (while technically American) cannot vote in the general election."

I think you have no understanding of what you are saying here. Your use of the word 'citizen' unless meant in the arcane way it was used after the revolution is misguided. We don't really think of people from New Jersey as 'citizens' of New Jersey but rather as residents of New Jersey. In the modern common parlance one is a citizen of a country and a resident of a state. While it is arguable that there may be an ethnic or cultural Puertorrican nationality no such thing exists legally. Persons born in Puerto Rico simply are US citizens, just like those born in Utah.

There is zero difference in the citizenship status of persons born in Puerto Rico v. that of persons born in say Pennsylvania. Puertorricans can vote in the general US election if they reside in a state, dc, or abroad, but a Pennsylvanian cannot vote in the same election if he resides in Puerto Rico. Thus it is not an issue of someone being "technically" a US citizen. What matters here is where they reside. The incredibly insane part of all of this is that Puerto Rico is a part of the US but its residents cannot vote in the general US election, however, were these same residents to move to France or China then they could vote in the general election.

So the question we should be asking is not why have US citizens that cannot vote in the general election vote in the primary, but rather how can we justify that US citizens living in the US, who are subject to US federal law, have no say as to who runs the federal government. It is not the parties' mistake to have a more inclusive and democratically accurate system than that of the general election, rather it is the government's mistake to not include the votes of US citizens in the general election.