This is only a guess from observation.
Paths records a number of paths for various contexts. The ones in Templates category are used when you
Templates or otherwise manage templates. LO builds a merge list of templates found in all the designated directories. You choose one in the dialog and it becomes the template base for the new document.
From poking in the XML, I saw that the full path to the template is recorded there. This is necessary to be sure to reference the correct template. Imagine you have two templates with the same name in different directories. If you keep only the filename, you create an ambiguity. Worse, you can modify the template path list. What would happen if you remove the directory you extracted the template from? So for safety the full path is there.
However, this full path is not written down iin absolute form but in relative form. The anchor point is the location of the document.
Consequently, if your dual boot does not change your file system architecture radically (i.e. the “essential” directories are mounted), it should work.
Usually, needed ancillary files end up in ~/.config/libreoffice/4/user/ and its numerous subdirectories.
If you manage to have directory ~ used for the user home directory in both OSes, this will be seemless. Otherwise, add a symlink on one side (or both) and have a try.
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