Did 1.0.0.1 also go down? The article doesn't say.
I've had sales teams pitch me on their authoritative DNS service running heterogenously, although I guessing both partitions gathered config from a single place, but we didn't get that far in the potential customer pipeline.
Of course, just because it's possible doesn't mean they're likely to do it.
That's my way of saying: it is seperate infrastructure
Remember that Cloudflare is probably the second largest DNS Resolver in the world. They aren't just going to tack two IP's onto the same system. The entire system would be completely independent for reasons exactly like what happened today.