That's a software problem moreso than a parsing problem. Plenty of software that uses regular JSON also strips unused data when writing back to a file it read

That's a software problem moreso than a parsing problem. Plenty of software that uses regular JSON also strips unused data when writing back to a file it read because internally it transforms the document into a data structure with no space dedicated for unknown data. It would be up to the software, or a very strict standard or library, to preserve unknown/unused data.