I think you're right ... I don't see how these figures are consistent. Maybe they're factoring in the time it takes to restore a copy, maybe 'normal redundancy' S3 is doing something clever, maybe it's simply another instance of Amazon being economical with the truth.
There is no proper math. 99.999999999% is a very silly number. The probability of all of Amazon's datacenters being destroyed in nuclear war within the next year well exceeds 0.000000001%.