Animated Transition: Lays a slide while a scene is getting transitioned from one to the other. Doesn't make changes the the scene.

Animated Overlay: Overlay places a transitioning image over the scene it is applied on. Does make changes to how the scene looks.

Look at this:

To apply Animated Transition:
Animations>Scene>Animated Transition

To apply Animated Overlays:
Animations>Scene>Animated Overlay

Applied together, it would look like this:

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