I see. The "encrypt home directory" option uses cryptfs to encrypt the file system,.LVM creates a volume group, and then you create physical areas for encryption, and then when you start the computer you unlock the volume group. It makes it harder to resize partitions (you do it via the CLI) but it is better because you are dealing with containers. There is performance lost through the cryptfs method as I believe it has to constantly encrypt/decrypt. If you just encrypt the /home it doesn't stop someone changing the binaries remotely, although this is not a concern for me. I think it prevents dual-booting though. It is best to wipe the disk for preventing metadata recovery, so it us recommended to use the whole thing and store data on other drives.
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