There is a github action step for setting config settings

https://github.com/Azure/appservice-settings

- uses: azure/login@v1
  with:
    creds: '${{ secrets.AZURE_CREDENTIALS }}'


- name: Azure App Service Settings
  uses: Azure/appservice-settings@v1
  with:
    app-name: ${{ env.AZURE_FUNCTIONAPP_NAME }}
    app-settings-json: |
    [
       {
          "name": "appSetting1",
          "value": "${{ vars.APP_SETTING_1 }}"",
          "slotSetting": false
        }
    ]