Sometimes it is necessary for a button’s clickable area to be larger than its visible graphics. It is common practice to define a clickable area that is independent of the button’s actual visuals. In such cases, invisible nodes used solely to control transform parameters are very useful.
Similarly, when creating a node for anchoring, this is a good example of that approach: How to GUI in Defold
In the past, developers often used a node with a small 2x2 alpha texture, which was neither convenient nor efficient due to overdraw. The visibility checkbox offers a much cleaner and more efficient solution.