Huh! So I think the plugin developer didn’t totally think this through, because the underlying Certbot program allows (though it doesn’t require) multiple webroots, which is normally appropriate when using multiple different domains. However, the plugin doesn’t seem to support this feature—with the single webroot field there.
Maybe the plugin developer didn’t know about that functionality and therefore didn’t include it in the plugin?
In Certbot, you can specify any number of -w options on the command line, and each -d option uses the most recent -w as the source of its webroot for that particular domain. When different domains host different content, this is required in order to make each domain pass the challenge!