That's inherent to the language specification, but it isn't inherent to the document. You have to have a system with rules that require that erasure.
Nothing prevents one from mandating a system that strips those comments out of JSON. You could even "compile" JSON to, I don't know, BSON or msgpack or something.
Just as nothing prevents one from creating tooling to, say, extract type annotations from comments in a dynamically typed language.
Agreed —— consider how comments have been abused in HTML, XML, and RSS.
Any solution or technology that can be abused will be abused if there are no constraints.
IIRC Douglas Crockford explicitly stated that he saw people initially using comments for a purpose like ad hoc preprocessor directives.
But what can we expect from a spec that somehow deems comments bad but can't define what a number is?