Yes you can. I keep my docs, downloads, email, iTunes, iPhone/iPad backups etc on a separate partition and use symlinks back to their original locations.
This way I could reinstall either from a clone or a fresh install and be back up and running immediately without having to re do all my email accounts, transferring of backed up docs etc etc.
As for difference what do you mean? Performance wise its likely to be slightly worse how much worse is debatable so it depends on your motives and what you want to achieve to whether it is worth it.