The article notes that DNSimple's ALIAS records avoid this problem. Would the same thing be true of CloudFlare's new "flattened CNAME" records?
I didn't see such a note, but I'm not sure it would be true, either. DNSimple doesn't actually implement a new DNS record type, it simply puts a TXT record on your domain that says "ALIAS for some.fqdn", and presumably it causes their DNS servers to do a recursive lookup for you (to whatever's in the TXT record) when you try and look at the A record for the naked domain. From github's DDoS prevention's point of view…
The TXT record is only there for informational purposes and could be removed without affecting the system.
Since we have an Anycast network you will also get a result that would be similar to a CNAME resolution, meaning you'll typically get a "close" set of IPs that would be similar to what you would get from the resolution of a CNAME, which ultimately resolves down to A records as well.