If we formally regard all organisms as 'varieties', then perhaps the macro/micro misunderstanding would be cleared up.
Darwin notes on p. 105:
A wide distance between the homes of two doubtful forms leads many naturalists to rank both as distinct species; but what distance, it has been well asked, will suffice? if that between America and Europe is ample, will that between the Continent and the Azores, or Madeira, or the Canaries, or Ireland, be sufficient? It must be admitted that many forms, considered by other highly competent judges as varieties, have so perfectly the character of species that they are ranked by other highly-competent judges as good and true species. But to discuss whether they are rightly called species or varieties, before any definition of these terms has been generally accepted, is vainly to beat the air.
What are the advantages of the distinction? Of classifying organisms according to genera, phyla, etc? The question perhaps sounds rather vacuous - of course labelling has utility. It allows communication. But what if the act of labelling things is actually causing a perceived either/or duality where none actually exists? What are the alternatives?