My 3D precomp doesn’t align in Z space with external 3D shape layer even using the same XYZ values

This usually happens because After Effects interprets transformations inside a precomposition differently than it does in the main composition. So while your Top view might show the precomp sitting behind another layer, the Active Camera could make it look like it’s in front which can definitely be confusing.

The solution is to enable Collapse Transformations for the precomp layer in your main comp. This little switch (the icon that looks like a sunburst) tells After Effects to treat all the transformations inside the precomp as if they belong to the main comp. When you enable this, the 3D  positioning will be interpreted consistently, and the precomp should align correctly with your external 3D layers.

Just make sure the precomp layer has the 3D switch turned on, and that any layers inside the precomp you want to interact in 3D space are also set as 3D. Also double-check your camera settings and renderer (Classic 3D vs Cinema 4D) because different renderers can affect how After Effects handles 3D positioning.