If they are different, then they are not the same scene. You can duplicate a scene, then click save scene as and choose another name. If the object is not a scene, and just a loose node, then you can click on a asset in the scene (such as the collision shape) and choose make unique. This will make a copy that you can change without the original changing.
This is done for optimization purposes. For example, if you have a game with 100 of the same asset (let's say an enemy sprite) and each one was unique by default, it would take 100x the amount of memory, additional processing for the physics engines, shader context switching, more load on transferring assets to the GPU etc. to the point where the game would be super slow. So the default behavior is the share/cache data unless the programmer specifically needs otherwise.