The FAQ has nothing to do with it. Nobody is contesting that cell tower location information is being used. The differing claim is this: the O'Reilly researchers claim that the co-ordinates logged are those of the device itself and these co-ordinates are possibly calculated using cell tower triangulation, while this blog post claims that the co-ordinates logged are those of the cell towers themselves rather than the device.
Because for a given timestamp, the iphone logs dozens of cell towers. So while you might be able to tell I was in Pittsburgh on Monday, you won't be able to figure out what address I was at.
but isn't the important thing whether or not these are public or private, and whether you have control over them? the precision of the location may affect some use cases, may not affect others, but doesn't strongly affect why this is important or not (on the other hand, it;s the kind of thing people can have a nerd fight over, which seems to be a big attraction...)