Yes because it was the section on gene evolution at the protein coding level: We next sought to use the chimpanzee sequence to study the role of natural selection in the evolution of human protein-coding genes..
Again, you don't seem to know what gene means compared to genome.
As far as your other point, yes, the initial report didn;t focus on this, but the second sister report, A genome-wide comparison of recent chimpanzee and human segmental duplications, was specific to these questions of chromosome structure.
On the contrary, you don't seem to appreciate that the genome is made up of genes, and sometimes, but not always, a substantial amount of other material.
On the contrary, you don't seem to appreciate that the genome is made up of genes, and sometimes, but not always, a substantial amount of other material.