Setup Folder does not get populated when using magento-deploy-ignore in Composer

Does anyone know why a composer setup like this could cause the post-cmd-install magento 2 base deploy to not fire correctly?

"extra": {
    "magento-force": "override",
    "magento-deploy-ignore": {
        "*": [
            "/setup/config/application.config.php",
            "/.github/PULL_REQUEST_TEMPLATE.md",
            "/pub/.user.ini",
            "/.user.ini",
            "/.gitignore"
        ]
    }
},

All other folders populate like pub and gihub, but not the setup folder.