I have read other threads on the subject and I don't think they have been 'shot down'. The fact you don't like the idea doesn't make it stupid. Would you rather face one massive guy in a fight or three smaller faster ones? I still think it makes sense to some degree. the separation only need take place in combat situations. In a future where FTL travel is common place and holograms become sentient, a ship like the Prometheus shouldn't pose any great technological barriers. Options in a fight are never a bad thing, plus, if things go awry do a runner and leave one section behind to cover your escape.