IMO, I think I feel like github should be ashamed for even making it possible to ask for blanket permissions. I think they should have designed their permission system to make it harder to do such a thing. Like maybe it shows a list of repos and asks "which ones, which permissions per, etc...". Not sure if that's enough but I think they need to do more.
As it is, the easiest path for a company to integrate with github is to ask for blanket permissions because then they can setup and/or add any hooks etc automatically. No work on the user's part. But, that contributes to making the entire infrastructure of the world less secure (because much of the world's infrastructure depends on these repos) and it feels irresponsible for github to indirectly encourage it.