While this isn't quite a solution, it is a workaround I've found.
If you navigate to the directory
Code:
/opt/ibm/lotus/Symphony/framework/shared/eclipse/plugins/com.ibm.symphony.standard.branding_3.0.0.20101015-2340/icons
(If you find that the directory I linked to above doesn't work, try searching for the file "symphony16.png" in Tracker search tool or another desktop search app and then open the folder in which it is found).
You will find a file called "symphony16.png". This is the image file which determines what icon will be shown in your notification area for IBM Lotus Symphony.
I found that by modifying this png file such that its background is of your panel's background image or color, the icon will blend in better to the notification area.
I set the png to dimensions 22px by 22px in GIMP (the dimensions correspond with whatever height your panel is set to), and then copied the panel background image for the theme I use as the background for symphony16.png.
See my attachments to view how the symphony notification area icon looks like now. Note that I also changed the icon itself.
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