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.