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Photoshop: Solid color fill, layer blend mode and smart objects

I have several layer groups (7)- each contains several layers with layer masks and different blend modes (multiply, screen, overlay, etc.) several layers also have multiple opacities. Works fine... until...

I created a solid color adjustment layer on top and applied color blend mode and a layer mask to apply to only part of an image. I convert this to a smart object and I lose the transparency on layers below.

However, If I create an adjustment layer directly below the solid color, move the layer mask down and clip the color fill layer.... the smart object works fine...

Very confused on when smart objects retain transparency and when they do not (when convert from multiple layers/groups, adjustment layers, blend modes and opacities)

I have added sample 1 and 2
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