99.9% uptime corresponds to about 2 hours downtime per quarter, if my maths is correct. If that is indeed the guarantee, based on the experience at my company, GitHub has failed its promise recently (or is getting damn close). I recall 2 decent outages in the past few weeks alone. It's making me begin to doubt if GitHub's reliability is appropriate for an enterprise service.
I'm not sure whether the uptime guarantee is 99.9% independently or jointly for each service, i.e. if service A is down for 0.06% and service B another 0.06% but not at the same time, will this count as overall uptime >99.9% or <99.9%.
Rereading the SLA, it looks like Github can have each service feature like issue, pull requests, git operations be down 0.1% and still not reimburse. In your head you might not account separately for each feature, but Github does.