I think the logic is that the current way isn't a big problem now that there is a standard of how you add your username to the file, and has allowed for some flexibility on the membership.
Have you read the issue? The problem is that the current way things are done requires manual merge requests because of merge conflicts resulting from the updated userlist array. The github api method is 1:1 with the requirements of joining the community and leaves no room for human error (unless the person in charge of pull requests does not standardize their own process for automatic merges).
