It's called the mcpi folder because if you were to download the original package linked by Mojang, it would be unpacked into a subfolder called mcpi.
On Raspbian and MATE, the built-in equivalent is
/opt/minecraft-pi so just use that. The tutorial you linked is fine... just note the folder is owned by root so you'll have to sudo some of those commands.
sudo apt-get install bspatch
sudo bspatch minecraft-pi survival ~/Downloads/survival.bsdiff
sudo chmod +x survival
For reference, the original thread by the guy who made the patch(es):