Your scenario sounds like multiple selection mode. The selection functionality of the VisualizationLayer mimics the extended selection mode. In a few words using rectangle selection will select only the items inside the rectangle and unselect the ones out of it.
What comes up to my mind is to use custom code to achieve this. I will use the VisualizationLayerItemsSelection SDK example, for example. Inside the LayerSelectionChanged event handler, I am removing the logic for setting the IsSelected property to false. This way creating the rectangle will select all items inside and don't unselect the others. A question here arises, how to unselect an item then. You could do this using an attached property. You can subscribe to the MouseDown event of the MapPinPoint.
For your convenience, I have modified the SDK example to demonstrate this. You can additionally extend this approach, so it covers all your cases.
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