Let’s say you have 1 button in one scene and 1 button in another scene and they have the same theme applied. If you change the theme slightly (example: adjusting font size) and save it, then this will be applied to all buttons.
But in many situations, you only want one button to be affected, so you make the theme on this button unique so all changes only apply to one button in that one scene without affected any other scenes.
Make Unique (Recursive) also affects all sub resources that are connected to the node that the theme is applied on. This is helpful in cases where you have one big Mesh with many materials attached to them and they all depend on the theme.