The problem is GitHub's permission system is bad. I'm not sure if the problem is that legitimate apps are required to request way more permissions than they wan

The problem is GitHub's permission system is bad. I'm not sure if the problem is that legitimate apps are required to request way more permissions than they want to get the ones they need, or if the prompts themselves are basically crying wolf all the time ("act on my behalf"? That could mean literally anything, why are you showing me that at the bottom of a list of other permissions? Doesn't it imply all the rest?). So the only way to use them is to either deny most legitimate apps because of scary permissions, or learn to click past the prompts to get your work done. If people do the latter due to a bad system then GitHub is not blameless here. They need to fix their system.