What I'm not understanding is why logging out or rebooting is required to keep a computer with full disk encryption secure. That's certainly not the case on competing OSes like Windows.
Usually in Linux the system is installed on an encrypted filesystem (cryptsetup, LUKS). Only kernel and so called initrd image (early boot stuff) is outside the encryption. The disk is opened at very early stage in boot when just about the kernel is loaded. Thus, the encryption is open whenever the operating system is running. Everything is of course still transparently encrypted on disk but the "lock" is open. One must shut down the computer to close the filesystem's encryption.
"Then click Install Now, and follow the rest of the instructions until you get to the “Who are you?” page. Make sure to choose a strong password — if someone steals your laptop while it’s suspended, this password is all that comes between the attacker and your data. And make sure that “Require my password to log in” is checked, and that “Log in automatically” is not checked. There is no reason to check “Encrypt my home folder” here, because you’re already encrypting your entire disk."
Above quote is from the section titled 'How to encrypt your disk in Linux' on the page at