Oh: yes, there are other ways to tell whether the windows are from the
same application.  The most immediately obvious ones are the optional
WM_CLIENT_MACHINE and _NET_WM_PID properties, which would give you the
process ID of the owning application:

http://standards.freedesktop.org/wm-spec/wm-spec-1.3.html#id2507760

Beyond that we'd be getting into window matching territory, looking at
title strings and icon bitmaps and so on.

-- 
alt-f6 doesn't reliably switch between windows within an application
https://bugs.launchpad.net/bugs/72732
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