YAML is good for simple configs. As the article says, JSON is much easier to programmatically generate than non-standard YAML. You still can store files in YAML, but compose and convert them into JSON in user data.
Again here, now you have 2 problems. Why not just go with a simpler config language and skip converting it and all the complexity that adds? It's possible to make this extremely complex, to the point where the config is in a database with ACLs and requires a DB server system (which itself requires config) to host (e.g. WebLogic) , but what do you gain?