Yep, everything in the engine exists in a 3D space. For 2D games you use an orthographic projection in your render script and for a 3D game you use a perspective projection.
Everything should always behave the same way regardless of platform and if it is 2D or 3D. For physics we use Box2D for 2D physics and for 3D we use Bullet (toggle between 2D and 3D physics in game.project).
Moving around freely in a 3D space is a bit more complex, but moving on a plane while using a perspective camera is essentially the same as making a 2D game.
But keep in mind that our focus has been primarily on 2D games so 3D is going to be a bit more low level. This fairly recent dev diary by @Epitaph64 will give you an idea of some of the challenges you may come across: Unexplored Territories Dev-Diary