@wbamberg
That is an odd situation which I had also enquired about long time ago.
While WebExtension manifest.json tolerates comments, since WE sees it as a JS object, strictly speaking JSON does not allow comments so it will be an invalid JSON.
Therefore, if manifest.json is regarded as a JS object resembling a JSON, then it is fine but as a valid JSON, comments are not allowed.
It is the same case with messages.json.
Finally, since the extension .json is used, one would think that it should adhere to JSON specification.