I think you are over thinking this.
If you have elements on 1 scene and you need to transition the bulk of whats on display then it makes sense to change to another scene.
This does two things for you as the creator. It helps you not have to create animation transitions on a load of elements like hiding them and showing new ones. It also helps keep things organised in manageable chunks.
Timelines are used pretty much the same way. They are a management tool.
Timelines help you break down what could be complex animations into manageable chunks.
We only ever suggest that you added something to it's own timeline in most cases because it makes it easier to control what is going on.
If you have a lot going on and all on one timeline you will start to get constrained by the linear time of that single timeline. You will then have to get creative with your timeline actions and property changes, making them repeat, jump, pause. When it looks like this is going to start happening then thats when you start thinking about adding a new timeline for some of the elements animations.
You then have other timelines that you can start a particular animation without interfering with the other timelines.
Note: I say without interfering with the other timelines. Naturally more than one timeline can act on an element at the same time.. ' wow man mind blown.. '
In both cases we are not thinking about performance and load.