I recently came across this PDF file stating that dom0 and the hypervisor (Xen) 
are stored unencrypted on the disk, because the disk wouldnt be able to 
boot(According to the PDF). but as far as I know, only /boot and GRUB are 
stored unencrypted.  so is this PDF file wrong, or was I wrong (or both?).

Here you have a link to the file, you can find it on page 7: 
http://www.cs.uu.nl/docs/vakken/b3sec/Proj15/QubesOS.pdf

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