My company is going to be installing this action once per organization in order to get submodules to work. I would really like to be able to point them to https://github.com/actions/create-github-app-token for the documentation, but step 1 is not very clear and I am worried that people will get confused about what permissions to request.

I am wondering, can you expand upon step 1 which says:

Register new GitHub App

Option 1 would be to list which settings we are supposed to check and uncheck, as well as which permissions we should be requesting.
Option 2 would be to follow the example of GitHub ARC in https://github.com/actions/actions-runner-controller/blob/master/docs/authenticating-to-the-github-api.md which actually provides two useful links that prepopulate various settings:

• Create GitHub Apps on your account: https://github.com/settings/apps/new?url=http://github.com/actions/actions-runner-controller&webhook_active=false&public=false&administration=write&actions=read
• Create GitHub Apps on your organization: https://github.com/organizations/:org/settings/apps/new?url=http://github.com/actions/actions-runner-controller&webhook_active=false&public=false&administration=write&organization_self_hosted_runners=write&actions=read&checks=read

Using GitHub ARC, it was really cool to be able to click one link and have it prepopulate the settings that it thinks I'll need.