The standalone mode is easy and works without requiring a web server, but it requires applications to stop/start the web server for the standalone server to run.
This can be improved by using webroot, that uses the web server that's already running to install/update the certificates.
The recipe could have an "auto" mode that would check if port 80 is available or not. If it is, use standalone. If it's not, check what application is using it (apache/nginx) and try to use this application as webroot.