Depending on the file which will be put into filesystem, as long as that file is not a malware, then that would be safe.
But don't worry to write/read file(s) to File System directory, cause you can tighten that directory security (include it's inheritance) by give a proper access right and security restriction. eg: read/write/modify.
By default, File System, Local Storage, and Storage directory are located on "\Users[Current User]\AppData\Local\Google\Chrome\User Data\Default" directory.
However you can customize it by using "--user-data-dir" flag.
And this is a sample:
"C:\Program Files (x86)\Google\Application\chrome.exe" --user-data-dir="C:\Chrome_Data\OO7" --allow-file-access-from-files
Hope this helps anyone.