BTW I don't know the reason, but you have a file named /etc/skel/Desktop this blocks Cinnamon from creating the Desktop folder (Can't have both a file and folder with the same name),. Easy finx is remove that file from your skel folder and it'll fix the issue, because if I turn on show desktop icons, it shows all your folders in /home/{USER}/ because it must default to that when not able to set the desktop path it wants to.
BTW I don't know the reason, but you have a file named etc/skel/Desktop this blocks Cinnamon from creating the Desktop folder (Can't have both a file and folder with the same name),. Easy finx is remove that file from your skel folder and it'll fix the issue, because if I turn on show desktop icons, it shows all your folders in /home/{USER}/ because it must default to that when not able to set the desktop path it wants to.
I tested this in a VM (so far) and I was expecting it to boot up like a normal Debian or Mint/Ubuntu distro, these take anywhere from 38 seconds to just over a minute to be on the desktop, I would really like to know more about your method to build this OS as it is the way I want to do it from now on, I've been using a base Mint OS and adding to that and using penguins eggs to capture it. But like I said, after trying your OS and seeing it is fully packed and can somehow boot up in 14 seconds, OMG,...