The name of the config folder is same in all systems so I just haven't seen any reason to make an exception for this special case.
It is not a standard way of doing this, there is already the .config folder which is hidden, why another hidden folder?
I'm not sure what causes the background color in the tray icon. Could be some incompatibility problem with its tray implementation since Rainlendar uses GTK. You could try to replace the tray icon with a larger version which should get rid of the white background.
Replacing the trayicon.png file with a larger one doesn't help, it gets resized.
Testing with some other apps like aMule (which uses wxwidgets) I see that it has also the white background tray icon.
Rainlendar2 doesn't use wxwidgets, right? Because I found this bug http://trac.wxwidgets.org/ticket/4810#comment:5
which says that wxwidgets doesn't use the native GTK+ API for the system tray (but now in trunk it does).
Maybe you are using an old implementation for the tray icon? I think this because many other GTK+ programs don't have the white background in the tray. Maybe this can be useful http://blog.sacaluta.com/2007/08/gtk-system-tray-icon-example.html