By far the easiest way to solve this problem for all skins is to apply "overflow: hidden;" to #mw-content-text. That is both skin agnostic (the element is output by the page output handler around only the wiki page content and nothing else) and water tight.

However the difference is that that doesn't just move content to its own layer, it also restricts its boundaries. Meaning, the skin interface isn't just on top of any content sticking out, the content sticking out will be invisible (cropped) at the border of the content area.

However I don't think that is feasible at the moment due to the large number of icons and semi-genuine use cases we don't yet provide natively (e.g. article quality icons, coordinates, interproject links etc.).

So for now the approach we've been taking seems fine (although this time it'll actually work), which is ensuring layer security. That way none of the skin interfaces are affected (e.g. logo, personal links etc.) however any empty space outside the wikipage content that isn't covered by interface components  (e.g. the space between logo and personal links, space between logo and first sidebar link etc. anything that is colored purple or blue in the screenshot) could still be hijacked, though it is much less frighting in those cases. And that can only be prevented if we completely crop content. Which we can't do until we drop support for positioning of icons such as Featured Article, and Coordinates to the top right of the article (just outside the content area, next to the title).

As crazy as it sounds, we can actually drop support for that relatively soon because we only have to drop support for icons positioned there from wikitext. Most wikis don't actually do that anymore, instead they give those templates a css classes, and move the icons to the "proper" place in the DOM outside the content area through site javascript. Though that is somewhat evil too, it is what we'd do in an extension as well. And from javascript, any changes uncontrollable anyway and must be presumed safe (due to user right restrictions).