If you change the gtk theme setting for xthickness/ythickness icons in the taskbar and in most panel items get their paddings modified, but the notification area just ignores these settings. Now, I think the notification area should make its best to be consistent with the geometry of other icons that stay at its side in the panel (mostly panel plugins, that look pretty much like typical systray icons). At least when there is no frame around the notification area that makes the separation clear.
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