“Auto” Panels are meant to have an object surround one or more objects. When that main object is a Shape, it can form a border around the other elements of the panel. https://gojs.net/latest/intro/panels.html
You can set or bind each of the non-main elements’ alignment property in order to arrange it within the available area of that main element. But you would then need to compute those Spot values if you want those elements to avoid overlapping each other. Using a “Horizontal”, “Vertical”, or “Table” Panel is a much easier way to arrange objects without overlapping.