If we just had this one piece of data to deal with, then it would make the most sense to say that the great apes are closely related and that humans diverged at some point before the viral insert appearing in the apes. However, the conclusion reached needs to supported by all of the data. The solution these authors propose succeeds in explaining all of the genetic data available.
You missed the point. The results of the experiment do not matter, since any result will be explained to fit the desired tree.