It would not be trivial because npm/yarn don't just read package.json but also modify it. See numerous GitHub issues in either repo about supporting comments inside package.json.
Of course nothing is impossible, but I think that the ship has sailed. I was just dreaming of what could have been :-) Subtle details in NPM's behavior would've probably been designed differently if it was necessary to make updates to the package file without destroying layout and context.
Stylistically, I agree with you as TOML is clean and well thought. Moreover, TOML has support for more data types that JSON lacks leading to ugly workarounds (floats as strings anyone?). The main advantage of JSON is that its encoding/decoding is included in JS as it is, and it's generally deeply ingrained in the Node community.