just because we don't have an explanation right now doesn't mean there isn't one.
That is rarely if ever the answer given, we frequently don't have a complete answer and an answer of sufficient depth to satisfy the ID proponents and creationists seems to be a logical impossibility, but there is usually a plausible explanation which is swiftly discounted by the ID/creation side. You seem to be similarly using 'plausible' to mean' complete and detailed in every aspect'.
And we would also not expect to find the first or only person who had such a rearrangement, but a representative of the population.
So is your question, "If an incredibly statistically unlikely thing happened might it lead us to make incorrect conclusions?", If it is then I'm not sure why you even had to ask.
That aside, if the genetic material was sufficiently well preserved that they could derive a karyotype from it there would be enough material to show that they were virtually identical genetically, so they might well classify it as a sister species or a case of incipient speciation.
Chromosome 2 is presented as evidence of human - chimp evolution (and I agree it's quite a strong piece of evidence) but if it is not a plausible explanation for the evolution of chimp - human, doesn't that still leave us without a plausible explanation?
You are conflating two distinct things here, the common ancestry of humans and chimps, for which Human Chromosome 2 is held up as a strong piece of evidence, and the general divergence between the chimp and human lineages and how it has given rise to the distinct modern species, in which the chromosome 2 fusion is only really of interest as one of a number of differences, and is not a particularly interesting one compared to many as it has been linked to no clear functional consequences.
In studies of hybrid infertility/speciation in Drosophila they have identified dozens of individual mutations each of which is sufficient to establish a strong barrier to reproduction between populations, but they can't all be the initial causative basis for reduced reproduction between the ancestral populations when they first split. Similarly there are almost certainly dozens of genetic factors which would prevent humans and chimps viably interbreeding including the differences in karyotype, all of these may constitute plausible explanations but that doesn't let us identify the chromosome 2 fusion or any of the others as the specific causative basis of the initial reproductive isolation of the ancestral populations.