Is it possible to make the elements dragged from the palette not to hide abroad? I just want the elements to be dragged onto the diagram without jumps.
Is the drag-and-drop working as desired from your Palette to your target Diagram? Does everything work the way that you want when the mouse/finger is inside the target Diagram? Is your question only asking about the dragging behavior outside of the Diagrams?
If so, it might be easiest to position the Diagram closer to the Palette.
If that is not possible, perhaps you could position a third Diagram between them. If a drop happens in that dummy Diagram, you could delete everything to keep that diagram empty.
And if that is not possible, you will need to implement drag-and-drop yourself.
Sorry, but GoJS only implements functionality within the DIV element. This is to avoid conflicts with other components.