There's no manipulation whatsoever. In fact, Google encourage website developers and SEOs to optimise/tidy their code and keep a good code-to-content ratio. This is why Google gives us so many tools in order to do so. It makes our sites easier to crawl for Google, and in return Google may even like us more for it!
Just found an article that sums it up quite nicely:
"Essentially what is being stated is a fairly logical conclusion: reduce the amount of code on your page and the content (you know, the place where your keywords are) takes a higher priority. Additionally compliance will, by necessity, make your site easy to crawl and, additionally, allow you greater control over which portions of your content are given more weight by the search engines. The thinking behind validating code for SEO benefits is that, once you have a compliant site, not only will your site be a better user experience on a much larger number of browsers, but you’ll have a site with far less code, that will rank higher on the search engines because of it."
- http://www.hobo-web.co.uk/official-google-prefers-valid-html-css/
But going back to your original post, "above-the-fold is dead", yadda yadda... So long as your content in the source is metaphorically "above the fold" and not drowning in heavy code, on the page itself just worry about giving your users the "experience" that they're looking for. And not how many pixels from the top of the browser your content is. Hope that makes more sense!