Hm, the MultiSceneNodeSample shows that using alpha values smaller than one work correctly. See screenshot:
The marked box is created in line 396 (all the colors have alpha value set to 0.3 a few lines above).
The screenshot shows that the objects correctly visible through this box.
Also, is the alpha value in line 364 is changed, this also works correctly.
The blending mode (AlphaBlend or Opaque) and the RenderingLayer (transparent objects are put to Transparent RenderingLayer so they are rendered after all other objects and are also sorted by their distance to the camera) are controlled by the VertexColorMaterial.HasTransparency property.
When the VertexColorMaterial is created by passing an array of colors to the constructor, then the value of HasTransparency property is automatically calculated by checking individual colors (for alpha < 1). To prevent this check (improve performance) you can also use constructor that also takes hasTransparency parameter.
You can also manually change the value of HasTransparency property.
If you first initialize the VertexColorMaterial with only opaque colors (alpha == 1) and later change the alpha values, then you need to call UpdatePositionColors method for the changes to take effect. If you have not manually set the HasTransparency, then the colors are checked again for any transparent color and HasTransparency property value is updated.
Anyway, if you have a case when this does not work correctly, please provide some additional information on how to reproduce that and what is expected.