Your issue could be called an issue of production pipeline. Play each tool to its strengths. PDF in this instance, while likely being your destination format, is also probably a poor format for your intermediate production needs. If you are happy with Inkscape in it's current role in your pipeline, ...

You do not need to convert it to paths, and in fact this breaks one of the key points of the tutorial. Inkscape does a strange thing in that it creates the linked offset _under_ the original. To illustrate this - Create a simple shape. Select it. From the menu select "Path" then "Link...