Why are you comparing renaming a file inside a directory picked or created by the user to robbers picking a pocket? It's quite typical to implement "atomic writes" by writing to a temporary adjacent file, and once the write is complete, move it to the actual destination filename, possibly overwriting the existing file. For example when exporting a video in a video editor, you might write it first to "$APPDIR/Trip to Spain.webm.incomplete" and then move it to "$APPDIR/Trip to Span.webm" once the file is valid.
I am fine if Firefox or any other user-agent mandates that the user can only grant write access to empty directories in order to protect their users from robbers. I'd still be able to build and organize a library of the user's data there, and they'd still be able to edit files with other native apps without needed to upload or download anything.
I think the remotestorage.io suggestion a little odd, since the only way it seems one can expose a local filesystem to remotestorage.io apps would be to ask my users to download, install, run, and secure a native, non-web HTTP server program, or to sign up for a third party hosting provider where the files will be off in a cloud. That does not sound like a "local first" app to me :(
I find it ironic that a protocol called "remotestorage" touts that it is offline-first design because it keeps user data in inaccessible user-agent storage until the user goes back online, at which point it writes that data to a remote storage provider. Only once the file is written to a 3rd-party server can the user can download the file back to their filesystem. Wouldn't writing a file to the user's filesystem be a more convenient and simple system?