Like I mention in the post, it's about consilience. Some of these things were indeed known, but added independent proof won't hurt.
Plus putting the whole mouse genome next to a human genome and comparing them in toto was not possible before the human genome project.
There were cases where the DNA said something slightly different to what more traditional methods said. There was a debate between paleontologists and molecular biologists as to when the split between humans and chimps happened, the former saying 15 million years ago, the latter saying 5 mya; the debate was won by the molecular biologists.
Understanding human diseases was one of the main goals of the HGP, but really it was in a lot of ways a goal unto itself, since the benefits could be many and varied.
Thank you for your input!