Usually a magazine overlays its title with a very dramatic photo of a person, which makes the person stand out. And usually only a few letters are obscured. Our brains are quite good at filling in the details.
I'm a lot less impressed by a fricking navigational toolbar that obscures the top of every letter of the logo. What remains are the less recognizable bottom halves of the letters. The T and I (not shown, but also F) look identical for instance. I'll believe that this is intentional, but I think it looks horrible.
That's because a magazine is printed and its appearance doesn't vary between people looking at it, so we automatically assume that it's supposed to look the way it does. A website can look differently depending on which browser is rendering it.
I see your point, but my Web browser is also an interface, and the way the top cuts the header off makes it look as if there is a rendering problem.
It feels to me a bit like a glossy magazine printed on good quality stock having a cover with a crease in it by design. Most would just assume they got a creased copy until the saw the others.