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.
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."