In my example there was a site navigation, not article navigation. And with article navigation, the same problem exists. The article should be before the navigation. But it's not practical at all to implement.
And what comes to skip to content -links, those definetly are hacks. What they mean is "Dear user, we would have put the content first in the source, but since CSS is not a layout definition language, it was not possible, take this link instead."
Actually, you can use absolute positioning to achieve what you want, in a fixed-width layout. You use CSS to add padding to the top of the content which is equal to the height of your navbar/header and give the navbar/header position absolute and top 0.
I haven't figured out how to do this with responsive layouts. It's never worked well for me but I will come up with a solution one day.