It shouldn't be a problem.
This kind of designs basically doubles your workload though, as you are effectively working on two different games at the same time.
If that is not a problem...
You could have a layout in which you explore the world in a top down fashion, when you find a dungeon in the over-world your game logic could go to a different layout in which the side-scrolling portion takes place.
When the side scrolling level is complete, by either winning or loosing, the game takes the player back to the over-world layout.
Different points in the main exploration layout could take you to different side scrolling layouts. It should work just fine.