I wish this myth would die. #000 is already dark gray on any normal real-life screen anyone uses because of ambient light, halos, etc. It's nowhere near "true black".
There is a good reason to avoid pure black or pure white in an interface, but it's nothing to do with "naturalness" or even legibility.
It's simply so that images or content which do include the full brightness gamut from #000 to #FFF "pop" in comparison. You want the darkest shadows and brightest highlights to catch your attention, and not have them compete with browser or interface chrome.
An interface is generally intended to "recede" next to actual content. But if your interface is star of the show? Use pure black and pure white. Go crazy. It's been used to great effect before.