I read the docs on About authentications as a GitHub App installation and it says:

This allows the app to access resources owned by that installation, as long as the app was granted the necessary repository access and permissions.

This line combined with your error "Resource not accessible by integration" seems to me a scope issue. Is it possible that the app is not given required permissions e.g. read/write or perhaps other admin related scope? How about re-checking the permissions?

Here's a doc specifically created for Dependabot but it might be helpful to you: https://docs.github.com/en/code-security/code-scanning/troubleshooting-code-scanning/resource-not-accessible