But yes, I think the thought experiment is seriously impaired by the fact that the existence of more copies of you is likely a bigger deal than whether they get dust-specked.
The idea was that your choice doesn't change the number of people, so this shouldn't affect the answer.
That seems, if you don't mind my saying so, an odd thing to say when discussing a version of Newcomb's problem. ("Your choice doesn't change what's in the boxes, so ...")
You're given the option to torture everyone in the universe, or inflict a dust speck on everyone in the universe. Either you are the only one in the universe, or there are 3^^^3 perfect copies of you (far enough apart that you will never meet.) In the latter case, all copies of you are chosen, and all make the same choice. (Edit: if they choose specks, each person gets one dust speck. This was not meant to be ambiguous.)
As it happens, a perfect and truthful predictor has declared that you will choose torture iff you are alone.
What do you do?
How does your answer change if the predictor made the copies of you conditional on their prediction?
How does your answer change if, in addition to that, you're told you are the original?