Assuming that the way these queries work has not changed since @Krinkle's comment in 2011, I would like to suggest the addition of a separate special page/query solely for non-existing template transclusions only in the main namespace. Currently, using WantedTemplates to clean up on pages in the main namespace (which is the one namespace where non-existent template transclusions are by definition unwanted) is incredibly inefficient by checking hundreds of pages just to see if the list of inclusions contains a main space article.

Problem seems to have been fixed. I haven't noticed this error pop up on the Dutch Wikipedia for a few months and found no Global User Pages lingering on the sample I just did on the top 5 wikis. I think this can be marked as resolved.