I discuss melatonin's effects on sleep & its safety; I segue into the general benefits of sleep and the severely disrupted sleep of the modern Western world, the cost of melatonin use and the benefit (eg. enforcing regular bedtimes), followed by a basic cost-benefit analysis of melatonin concluding that the net profit is large enough to be worth giving it a try barring unusual conditions or very pessimistic safety estimates.
Full essay: http://www.gwern.net/Melatonin
The presence of melatonin in the body and its function there may be fundamental, but that does not make the effect of supplements equally fundamental. The role of vitamins is also fundamental, but you yourself cite evidence that vitamin supplementation for all is a bad idea. I don't see anything in what you have written to suggest that melatonin supplementation for all should be any different.
FWIW, I have tried melatonin -- last night, in fact, 3mg -- and observed no effect. I did not fall asleep more quickly (I was still awake three hours later, at 01:40); I woke at a typical time; my waking lethargy was, if anything, slightly more than usual; my dreams were typical.
I'll give it a few more goes with a reduced dose (from further reading, 3mg seems excessive), but real science is supposed to work every time.
ETA: 1mg had the same lack of effect.