That’s not what scene.apply does. The scene.apply action is more like a shorthand way to have a collection of entities change to new states that were not previously configured as a scene in parallel and with the option of a transition duration. It has almost nothing to do with scene entities.
From your description I think you just need to use scene.turn_on with a transition.
“Scene: Activate” is how scene.turn_on is shown in the UI Editor.
FWIW, if you just paste scene.turn_on in the “Add action” selector it will eliminate everything that doesn’t match. As shown below, searching for scene.turn_on returns the correct option i.e. “Scene: Activate”.
The former includes transition and the latter does not. It’s kind of puzzling, but that’s where I was messing up and got it confused with Scene: Apply (that also has transition).
That’ll teach me not to do automation’s when I should be sleeping.