Packer and Yaourt use /tmp.
Is there any way to update without recloning or manually setting up a folder for the PKGBUILD?
Packer uses whatever your $TMPDIR is. So you can do
TMPDIR=/whatever/path packer -S foo-pkg
Alternatively, you should not be cloning the entire repo, just --depth=1
Is there any way to git pull from yoaurt/packer/etc?
Yaourt uses makepkg. Try setting, in /etc/makepkg.conf, a path in PKGDEST and SRCDEST and then, in /etc/yaourtrc, set "EXPORT=1" and "EXPORTDIR=" (yes, empty)