I felt the article pretty thoroughly explained why the author feels that hives are not currently respected as an extended phenotype. Many studies of bee behavior are run on bees in artificial hives. They are treating artificial hives as interchangeable with their natural equivalents and assuming that the behavior observed reflects normal bee behavior. This can lead to many erroneous conclusions, the same way you might get misleading studies on beaver behavior if you studied a bunch of beavers living in a rabbit hutch. To quote from the article:

> Honeybee (Apis mellifera) colonies don’t hibernate. In the wild they overwinter in tree cavities that keep at least some of their numbers above 18°C in a wide range of climates, including -40°C winters. But popular understanding of their overwintering behaviour is dominated by observation of their behaviour in thin (19mm) wooden hives. These man-made hives have very different thermal properties compared with their natural habitat of thick-walled (150mm) tree hollows.