The article you linked is OK, but your use of the word "considerable" and the implication that there is some startling new problem for evolution is nonsense.
What is interesting is that the coding reagions of DNA are mor similar than the non-coding. This is what you would expect if variation is subject to selection.
The article concludes that this is a paradigm shift. Which by the way, I wish evolution proponents would read or acknowledge TS Kuhns work on Scientific Revolution which explains how scientific communities maintain consensus on theories such as evolution. The manner in which evolution advocates speak is inconsistent with historical scientific practice.
Moreover, the desire to see similarities between primates and humans so as to affirm the theory of evolution obstructs the view of differences. The study references these differences and is arguing that the 98% is inaccurate or irrelevant because we can now look at genomes in precise ways.
A comparable analogy would be going from a computer screen resolution of 256 colors to thousands. The possibilities of differentiation are much greater. Those differences are useful. Stigmatizing the observation of those differences hinders the scientific process.