That wouldn't be that hard to explain. It probably sounds like I am reaching for explanations. It would really muddy up the water though as far as the DNA analysis goes. Just to clarify, I haven't formed any opinions on any results and I am just speaking hypothetically. It would be very surprising to me to learn that they are closer than a Neanderthal if that is what the evidence actually shows. Even if that were true, I would still suspect that more ancient DNA might be there or essentially they didn't lose some of their "wild" characteristics even after hybridizing with our ancestors over the past few million years. I could actually see that happening if a creature was evolved to live on the periphery of a more dominant species. That could be something that would be very difficult to see in even a whole genome.
The bigfoot isn't necessarily going to be close to a human because it contains human mitochondrial DNA. That would imply though that they are close enough to breed successfully with a modern human at least occasionally. If it happened many generations ago as is implied by the widely spread out samples, from what I understand, it could be possible that the original modern human nuclear DNA was so diluted that it isn't even significant. There are many examples of hybrids with more than a million years separation and I believe that extends to a few million years in some cases. All you need to get the mitochondrial DNA is to have a female modern human somewhere back in the lineage. If that original hybrid were in the last 200,000 years it would most likely be in the range of modern humans as far as the mitochondrial DNA goes.
Mitochondrial DNA doesn't really have any effect on how we appear. It is just involved with metabolism. The mitochondria is like a fuel cell that provides energy for cells and the DNA of the mitochondria contains a subset of some of the genes that are needed by the mitochondria to function. Some of its genes are provided by the nuclear DNA. That probably makes it less likely for a very divergent mitochondria to function well enough to be selected for. That would be the logical assumption of why it would become the dominant mitochondria of a population. The other possibility is that BF is descended from the small original hybrid population and has a very compressed genome. I am not jumping to conclusions. There could be others with more divergent mitochondria. I was just speaking hypothetically about how a population could evolve by natural selection our mitochondria without being that closely related. It is possible that our mitochondria gave them an advantage so the others with other mitochondria died out. There is apparently some fairly strong selection for specific mitochondria. That is how we as modern humans all share a common female ancestor about 200,000 years ago. If not for selection pressure, the other mitochondria that existed 200,000 years ago would still be around. The point of that rather confusing statement was our mitochondria might have been an advantage and was selected for like a good genetic characteristic would be. That is how it could become widespread in the population without them necessarily being that closely related to us.