The PointTemplate is applied only to the Point geometries. This is because only there is meaningful to define a custom visual. The other geometries are some shapes so if you replace their visual representation you are losing the idea of using geospatial data. If you want to add some custom visuals you can use the Items collection of the VisualizationLayer and add FrameworkElement objects like Path, Border, etc.
As for the fill of the multiline geometry, this happens because the ShapeFill property of the layer. If you want to remove it you can set the ShapeFill property of the layer to a new MapShapeFill object with a transparent Fill and some colored Stroke.
I hope this helps.
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