@Ignostic, no we not yet sure it is an artifact. As we stated, and they stated, these cases are “ambiguous.” We do not know from evidence yet what they are. When we get more evidence, I am sure someone will look again.
No one has assumed anything. We said “we do not know yet, but think it is missing data.”
Probably less than 90%, as the human genome is around 90%. Just recently new technology is allowing for sequencing of full chromosomes. So this could change in the near future: First Complete Sequence of a Human Chromosome.