For example, I trialed major security vendor's enterprise product. They required their app be granted Admin on the GitHub org. All they needed to do was create issues, PRs, and read source code for analysis. There are scopes for that.
I was eventually on a call with a principle engineer in this company, who kept saying they needed this permissions, and I kept showing him the API docs that showed that wasn't so. Eventually he said, "well, we won't _use_ all those permissions, so just give them to us anyway, because it's easier this way." Sure, I'll give you the ability to change all my code, add/remove users, drop repos... etc, and trust that some day, when you're hacked, someone will not use those over granted permissions maliciously?
Security is hard. Be careful what permissions you give your 3rd party GitHub integrations.