GitHub provides the GitHub MCP server we're discussing right now. That tool allows interactions that violate the access control constraints defined by GitHub itself.
If you wired up "some other automated tool" to the GitHub API, and that tool violated GitHub access control constraints, then the problem would be in that tool, and obviously not in the API. The API satisfies and enforces the access control constraints correctly.
A Jenkins build server has no relationship with, or requirement to enforce, any access control constraints for any third-party system like GitHub.
If you wired up "some other automated tool" to the GitHub API, and that tool violated GitHub access control constraints, then the problem would be in that tool, and obviously not in the API. The API satisfies and enforces the access control constraints correctly.
A Jenkins build server has no relationship with, or requirement to enforce, any access control constraints for any third-party system like GitHub.