I love it when questions contain the research for their own answer.
The paper describes a particular set of genes:
We have identified a Y-chromosomal lineage with several unusual features. It was found in 16 populations throughout
a large region of Asia, stretching from the Pacific to the Caspian Sea, and was present at high frequency: ∼8% of
the men in this region carry it, and it thus makes up ∼0.5% of the world total
It analyses it current populations statistically, using a couple of approaches to conclude:
The origin was most likely
in Mongolia, where the largest number of different starcluster
haplotypes is found (fig. 1). Thus, a single male
line, probably originating in Mongolia, has spread in the
last ∼1,000 years to represent ∼8% of the males in a
region stretching from northeast China to Uzbekistan.
It considers, and shows evidence to refute, a number of possible causes of this, e.g.
Could biological selection be responsible? Although
this possibility cannot be entirely ruled out, the small
number of genes on the Y chromosome and their specialized
functions provide few opportunities for selection
(Jobling and Tyler-Smith 2000). It is therefore necessary
to look for alternative explanations.
It searched for confirmatory evidence by looking at a population that are (putatively) direct male line descendents of Khan.
Looking through Google Scholar, I can see no examples of refutation, but many others citing their results positively (e.g.). The paper was published in a reputable peer-reviewed journal, and contains a number of authors from prestigious institutions that are working within their areas of expertise, so the idea that it might be exaggerated for publication is unlikely.
It appears to have a robust result, that it seems reasonably to provisionally accept unless counter evidence is produced.