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Superfluous element isn’t wrong in terms of accessability, it might no be semantic and it does mean more code for something CSS should be able to handle (true, flexible layouts).
But usally, those superfluous elements means less code in the aftermath, since I tend to work with flexible or elastic layouts (according to w3c recommendations) and generally DOM-scripting or a lot of CSS-hacking is required for pixel precision.
Sidesection should go after the #content, in the source order at least, if it contains such an amount of links that it would be tedious to tab through, or browse through.
I’m a bit confused by the naming of elements. Most of them are named after appearance, not function.
#side might not at all be located at the #side. Another name, such as #resources (site resources) or heck, even #toolbox would be more suitable in the end. It’s self-explanatory really. Name elements after function, not visual location or appearance. This is the very reason why I would name things to .inner instead of .padding (since it might not all supply a padding attribute).
Just my 2 cents.