#mw-data-after-content doesn't have any styles to keep it from overlapping the sidebar, so any content in it easily winds up doing so on pages short enough to have the sidebar still present at end-of-content.

As an example, the following page doesn't overlap because it's long enough, but either the block shouldn't be full-width like that, or it should be forced to appear only after the sidebar ends even on shorter ones:

Replication steps

Add the following to LocalSettings.php

$wgHooks['SkinAfterContent'][] = function ( &$data, $skin) {
        $data .= '<div style="background:red; padding: 20px">SkinAfterContent</div>';
};

Note the overlap here:
https://skins-demo.wmflabs.org/wiki/Main_Page?useskin=cologneblue

Expected: they should not overlap