That all looks pretty good! I don't think it's the scopes, I often get a message like that if I've created the PAT myself without using create_github_token().
It's a little strange that you don't have an upstream in the GitHub project area, so that would be my first guess. This other community post says doing a manual push with -u will help enable the buttons, probably because it adds that upstream reference. I think you could also add an upstream with the use_git_remote() function from usethis.