Why does it matter that AWS is 99.95%? "Cloud" based services like AWS and AppEngine have more relaxed SLAs. GitHub is not a cloud service, its a centralized version control repository. And the 4 9s, well that's just something I've always strived for when providing a service but I do believe we should all hold ourselves to it.
Another factoid is that Amazon Web Services (AWS) only offers a 99.95% SLA so where did the 99.99% for GitHub come from?