When I start a new project with GitHub I always struggle with the same issue. When I create a GitHub project it's already prepopulated with some files (.gitignore, LICENSE, README.md) and hence with an initial commit. I explicitly choose to add these items so I don't have to care about writing them myself.
On the other side, when I start a new Xcode project it works in a very similar way: Xcode creates an initial commit with some files. So when I'm trying to pull my GitHub repo I always have to deal with Git refusing to merge unrelated histories problem.
Is there a correct workflow for this?