According to my understanding, you want to modify the order of installed directories in the installer. What you are experiencing is an expected behavior. As of R2022b, MATLAB organizes the order of all the included directories and you cannot change it.
Although if you want to modify the code included in your app, follow the steps mentioned in this link after updating the code: https://www.mathworks.com/help/matlab/creating_guis/app-modification.html
