Your screengrabs don't give away much, because they only show one layer, and you haven't revealed the Position parameter in the timeline so we can't see where the layer is positioned in space.
After Effects 2D layers appear in the order they're stacked in the timeline. Layers at the top of the stack appear on top of layers at the bottom. Just as they do in Photoshop, Illustrator, Premiere Pro etc.
After Effects 3D layers have X Y and Z position values, allowing you to position them in 3D space. A layer's position in space determines whether its in front of another layer, rather than its level in the layer stack. So, assuming your 3D camera is in a conventional position in front of your layers, a layer with a Z value of 200 will appear behind a layer with a Z value of 100. A layer with a Z value of 10,000 will be way off in the distance, while a layer with a Z space value of -200 may be so far forward that you (or the 3D camera) can't even see it.
As soon as you switch your layers to 3D, you have to think about their position in 3D space, rather than their hierarchy in the timeline layer stack.
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