When you create anything (scene, note bookmark, etc.), it’s added as a child element to whatever the currently selected item is. You have a scene selected, so the new scene is added as a child to that scene. You need to select the containing folder and add your scene to that. If you then want to change the position of the new scene – to move it above a certain scnee, you use drag and drop.
The structure is deliberately flexible. You decide how you want to use it. Some users might only add scenes to folders, others might have older versions of scenes as children of a parent scene. It depends what best suits your workflow.
Adding a scene or note above another scene directly – I’ll have to think about it, as it would involve 6 new menu options (scene, note, folder, bookmark, etc.), and then someone will want an option to add below, not above (6 more menu options)… I’m not sure.