[At the risk of forking the thread] to use the various functions CloudFlare provides that GH Pages doesn't. In my case was so that we can have multiple admin accounts to manage the zones, billing etc. because we're also using CF for domain registration, but also for things like stats, DDoS protection and other things.
The reason why I posted here was becuase I (naively) thought the default condition of having the CF proxy in place - which worked just fine at first - was going to work 