What’s their evidence that it’s #1, and not #2? I read the links but I still don’t see a reason why. I’m not saying it is #2, just that as you said:

They did the analysis on the samples that they have. It’s not like they could travel back in time and take a genetic sample

Yes, which means that the only populations that are “visible” to this technique are the humans that left descendants to the modern day. Maybe there were other populations that didn’t leave descendants to the modern day, specifically because of competition with other humans (but which would have survived, if not for the competition for their same niche).

Again, I’m not saying that that did happen. Just that it instantly jumps out based on a cursory reading of this that it sounds pretty possible, and I’m curious to see if there’s an explanation for why it’s not possible.

Also, outside of this article, the same evidence is cited along with how it is known that there was probably a huge population collapse thanks to other pieces of evidence.

I’m sure there was a huge population collapse; as I understand it, that’s an established fact based on a sudden absence of humans in the fossil record. But, it’s a very different statement to say “there was a population collapse” versus the statement “there was a population collapse down to 1,280 individuals.” One is not proof of the other.