No Safe-settings changes detected when creating pull request with new sub-org/repo settings

## Problem Description

### What is actually happening
When creating a pull request with a new sub-org or repository configuration, the safe-settings validator says that there are no `No Safe-settings changes detected`.

### What is the expected behavior
It is expected to see the list of repositories covered by the sub-org/repository configuration being modified/created.

### Error output, if available

## Context

### Are you using the hosted instance of probot/settings or running your own?
Self-hosted

### If running your own instance, are you using it with github.com or GitHub Enterprise?
GitHub.com

#### Version of probot/settings
2.0.17

#### Version of GitHub Enterprise