The reason for that was eventually these headers became real standards and software would break when the X was removed. I very much doubt we will ever see github api headers added in to nginx and apache.
So if your header is something you think should/will be standard but it's still in beta/testing, give it the real name.
Author here. We just wanted to be consistent here with other GitHub-specific headers prefixed this way. We could have had different headers with different formats or tried to change the formats of the old headers, but we figured this was the sanest way.
