Removing comments from JSON because some people might use them for parsing directives was an overreaction. The alternative always presented is to pollute your objects with "comment" values which, unlike actual comments, take up space and need to be parsed or filtered. Just imagine how silly it would be in any other language for comments to be replaced with variables.
And... nothing is stopping people from adding parsing directives in JSON itself anyway.
Actually it isn't. That was left as an afterthought and IMHO as a trick to try to ride the coat tails of JSON. YAML in the wild is a god-awful mess that bears no resemblance to JSON. To me YAML's only purpose is to enable lazy people like me to take notes in a text editor with code folding and syntax highlighting.