Hey! So, this project looks really interesting. I work at GitHub on the Partner Engineering team, we'd be happy to help guide your implementation to follow our best practices and help drive its success. Feel free to reach us at partnerengineering@github.com!
This GH app, for instance, received similar feedback and its author removed the offending scopes without losing functionality: https://news.ycombinator.com/item?id=11261953