If you're loading scenes, and you need the objects in different locations, perhaps just treating them as different objects would be best. You can make the atlas persistent by creating a sprite in the scene far away somewhere and invisible to the main view, and marking as Don'tDestroyOnLoad. The largest overhead will be loading the atlas, and if it is already present, setting up a few sprites will take no time all.
Not to mention, the workflow will be a lot smoother like this.