According to the current spec,
http://w3c.github.io/webcomponents/spec/shadow/#active-element
Document.activeElement returns "adjusted" element, i.e.
when the real focused element is within a shadow tree, it returns
the top-most shadow host in the Document treescope.

The real focused element can be retrieved by recursively applying
.activeElement against shadowRoots on the way, but it may be
convenient to have a way to directly retrieve the element from Document.

One use case is for accessibility plugins; when a web app is provided
as one custom element (e.g. <topeka-app> at https://polymer-topeka.appspot.com/),
Document.activeElement always points to <topeka-app>,  which does not make
much sense for accessibility plugins.
It may be also necessary to have another type of event than "focus", which
fires when Document.activeElement changes.