While in Xinerama mode there is a single large display covering all the physical screens. Calling to Toolkit.getScreenSize() leads to simple quering X for the size of this large display.
So I think this is not a bug. Nevertheless, we probably should correct JavaDoc for Toolkit.getScreenSize(): in the multi-screen system the size of the default screen (not the primary) is returned. For the Xinerama mode default screen is the whole large screen spread on all physical displays.
If one do need to deal with physical screens while Xinerama mode on GraphicsEnvironment, GraphicsDevice and GraphicsConfiguration should be used.