For clarity I've removed the first image (since it's a WIP sprite and is confusing the issue). The vanilla underground belt renders on top of whatever modded sprite is added to the vanilla loader entity.
Edit: Here's an image that perhaps is more clear:
In this case, the mod is Loader Redux and the vanilla underground belt entity renders on top of the modded loader entity.
Ok, I added structure_render_layer to loader prototype for 0.17.3. It defaults to current value "lower-object", underground belt and splitter structers use "transport-belt-circuit-connector"