Problems are that some tools will rewrite the file and reorder the "comment" away from what it's meant to comment on. Also might complain the "comment" item isn't expected there. I seem to remember package.json suffering from both of these under the control of npm.
Yeah it's definitely a limited solution, and I prefer that JSON be kept simple that way. Many package.json-adjacent configs like the Babel stuff can be in .js files, giving you comments and everything.