Comment 1 for bug 1483798

To expand on this a little, using a custom launcher the sub-window always gets filed with the main chrome launcher. For example, I'm trying to use hangouts, and while the Hangouts launcher will correctly launch the Hangouts app, it'll file the new window on the main Chrome launcher.

Checking the WM_CLASS via xprop I see:
WM_CLASS(STRING) = "crx_knipolnnllmklapflnccelgolnpehhpl", "google-chrome"

I've used the same *.desktop launcher for Cairo-Dock, Docky, & Unity... Here are the results:
Cairo-Dock: Launches window, files it (incorrectly) with the main Chrome launcher, and (incorrectly) uses the main Chrome icon in the sub-list
Docky: Launches window, files it (incorrectly) with the main Chrome launcher, and (correctly) uses the Hangouts icon in the sublist
Unity: Launches window, files it correctly in its own launcher, and uses the correct icon.

So there's enough info for the dock to do it in a better way.