GPG and PGP both make tempfiles, as do many of the email integration systems that use PGP, but I'm not here to help harden your idiosyncratic Linux setup, only to explain that your expectation that the OS designers are going to make 3rd-party crypto packages a priority is unrealistic.
If you need crypto-level assurance for your machine, you use full-disk encryption --- or at the bare minimum you turn off system restore points and use secure deletion software. People who harden Win64 professionally know to do this stuff, just like people who harden Linux setups professionally know the rest of the problems with your EncFS system.
I'm a security person, and not a Windows user, and I prefer the Win7 approach over the "whatever makes TrueCrypt easier to write" approach.
If you need crypto-level assurance for your machine, you use full-disk encryption --- or at the bare minimum you turn off system restore points and use secure deletion software. People who harden Win64 professionally know to do this stuff, just like people who harden Linux setups professionally know the rest of the problems with your EncFS system.
I'm a security person, and not a Windows user, and I prefer the Win7 approach over the "whatever makes TrueCrypt easier to write" approach.