Protect folders and files from unhautorized changes managing filesystem permissions.
On Windows surely NOT, on other systems maybe. AutoCHMOD intensively use the PHP chmod command: if this funcion is usable on your system, AutoCHMOD would run just fine.
Maybe, or maybe not. You must double-check the configuration of the permission you'll grant to your file and folders: if the configuration isn't correct for your server, WordPress could not run anymore and you'll need to restore the correct permissions manually. In future releases I'll try to check the configuration BEFORE applying it.