The File System API is a JavaScript API, not an HTML one, so it helps to think about it from that light (programs, not documents). The API allows tools such as photo editors, file converters, code editors, and the like to be given access to a set of files they can work on directly rather than needing to import and export from the browser on every change. If the attack surface is too much for a use case it can be globally denied by default in every major browser so you won't even get prompted.