I think this would be a good idea. "user:email" should be "more" unique than the username and would make it possible to identify a returning user even when the access token changed.
As I understood from the RFC the access token can expire and can be reissued anytime when the OAuth service decides to do so. A token change does not mean the user changed anything or intentionally revoked and reauthorized an app.
I understand Phalcon's point that it should not be possible to get access to old messages if a user closed his github account and another person registers at github with the same name. But there has to be some kind of unique id in the github database, I don't want to believe that their database primary key is the user's name.
As I could read in the github API docs there seems to be no way to retreive their internal user id so using "user:email" sounds reasonable to me.
(By the way my primary interest is NOT to change the phalcon forum or criticize the developer's decisions. I'm just developing a "Login with ..." service for a phalcon based community myself and I try to understand the phalcon forum oauth2 phps. In my case one of the OAuth services used should be Facebook and Facebook returns their unique userid which makes it much more simpler to identify returning users even if access tokens change.)