dzen has a nice -dock option that "sets some EWM (Extended Window Manager) hints that mark dzen as a panel/dock application". This is nice if you e.g. don't want compton to draw a shadow on the notifications.
You can see how dzen does it here: https://github.com/robm/dzen/blob/master/main.c
I've been investigating this issue and it doesn't looks like it would be semantically acceptable to mark it as a dock.
Please see _NET_WM_WINDOW_TYPE_DOCK on http://standards.freedesktop.org/wm-spec/1.5/ar01s05.html.
It makes sense to configure this on compton itself or perhaps changing compton's default behaviour not to apply shadows when the window type is a _NET_WM_WINDOW_TYPE_NOTIFICATION, as dunst windows are.
You can use the shadow-exclude = [ "n:e:Notification" ]; configuration on .config/compton.conf, or if you really need fine-grained configuration use the name of the window using #167 `s branch.
shadow-exclude = [ "n:e:Notification" ];
We could perhaps mark this as closed. /cc @knopwob
Sorry about the late response. I'm happy with that solution, so I'm closing this issue.
@hanschen You should be able to use #167 on master now that it was merged.
Thanks for working on #167 @badosu, that was one of the things I missed from dunst.