No, we don't understand every little genetic sequence, but we can compare sequences for differences. We've done a LOT of phylogenetic work with other species; the only difference here is that it's a Homo-type primate. This really, to be honest, is nothing new technique or scientifically. It's just a new sample offering new information. The scientific community has been doing things like this for years.

Generations of inbreeding could be what caused the divergence, yes...but that does NOT mean that what results is not a separate species. Really, in breeding is what ultimately causes the development of a new species. Say you have one Species called the Beaver-Ox. A couple herds of Beaver-Oxen become trapped in a Valley high up in the mountains by a catastrophic land slide blocking the only exit accessible from the valley. Over time, the two herds interbreed and interbreed and in breed and in breed. A couple centuries down the line, a scientist comes along and samples both the original Beaver-Oxen that are scampering around the base of the mountains, and then the Valley Beaver-Oxen and discovers they have diverged into different species due to genetic constraints and possibly environmental differences and differences. Perhaps the Valley is colder, so the new Valley Beaver-Oxen have longer coats. Maybe they are also smaller and hardier with a lower reproductive rate due to their decreased habitat size, and have developed a resistance to a particular mountain disease that used to only affect the Beaver-Oxen when they'd be passing through the mountains.

Anyway, point is, "inbreeding" does not mean that these scientists are wrong in the slightest.