If you need to see the two scenes while the transition is active, you have two options:
1) Make a screenshot of the current scene, put it on a fullscreen quad, unload the scene, load the next behind and do what you want with the sprite and the next scene's viewport.
I would choose this solution if your scenes are really big, as it doesn't requires twice as much memory. Otherwise, I would do 2).
2) Load the next scene under a Viewport node so you have the two scenes loaded at the same time, but rendering on two different viewports. Then all you have to do is animate those viewports, blend them together with a masking shader, slide their rect etc.
I never experimented with Viewports, but I think that's what you are looking for :)