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I think many of these classifications are caused simply by doctors refusing to say "I just don't know" and patients refusing to accept that they really don't and probably never will...
Take IBS. We are supposed to believe that there is a disease with no known cause, so many possible triggers and influencers that anyone can find some that fit and wildly varying symptoms... something similar could probably be said for many other "syndromes". Of course all of those people have something else or a combination of something else but nobody wants to admit they just don't know and everyone wants a diagnosis.
IBS is also a more generic condition with Crohns and Colitis being related conditions with identifiable physiology and treatments. The "cause" isn't known but it's similar with genetically susceptible individuals having environmental, bacterial, immune factors. Immunomodulators being frontline treatments.