Transform effect(pos. and anchor) does not repect layer hierarchy in Essential Graphics

Thank you for reporting this. I see that something is not right with the Position and Anchor Point for the Transform effect inside a graphic. Video effects that control the positioning of a layer will conflict with the transform properties of the layer itself. The Transform effect is one example. Basic 3D is another. As you found out, you can’t use that sort of effect inside the middle of a layer stack and get exactly the results you want. So it's best to use the transform controls for the layer itself, which you can see in the Essential Graphics Panel as well as the Effect Controls Panel.

If you really need to use the transform effect on a Graphic layer, like to get to the skew controls, notice that if you change one of the other controls first (like skew) and then change the position or anchor point, it applies only to the layers below, as expected. That may be a workaround for you.