Thanks guys! I'm quite aware of the em and it's history (design degree), but I'm sure others may find it helpful :)
As far as the 1em = 1px, I don't see how this is undesirable. The em is square, regardless of your units (be it points or pixels) and nobody would set their type at 1px (just like nobody would set printed type at 1pt). Furthermore, even your article concedes that in most digital typefaces, the capital "M" is usually smaller than 1em, and that the em is merely a reflection of the point size (48pt type would render a 48pt by 48pt square for the em, 12pt type would yield 12x12, etc.)
Besides, the reason people would do this would be more for setting dimensions of other elements on the page so that everything scales nicely when the user adjusts their font size. Sure, there will always be the rare few who set their default to something other than 16px, but well worth the price to pay for a pixel perfect layout that scales nicely.