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 result is the same: an A record lookup points to their IP. They don't know that you got there by way of looking at DNSimple's servers and their ALIAS technique.