(Apologies, I hastily commented on https://github.com/canonical-web-and-design/snapcraft.io/issues/2849 before realizing that discussion had been intentionally redirected here for visibilty.)
I’m very interested in this – I want to maintain my Snap on GitHub, but I cannot authorize snapcraft.io with admin access to all the repositories I have access to, so as far as I can tell my only option is to create a new GitHub account with access to just the organization/repository I want to grant access to so that I can authorize it, just so that snapcraft.io can install a webhook on my GitHub repository which I would happily configure myself directly without all this hoop jumping if it were an option.
So in my case, I want to use GitHub webhooks, but cannot reasonably authorize snapcraft.io to access all the organizations on my GitHub account.