Hello,
I'm not sure if this will help, but you can try to configure your repackaged setup not to display an entry in "Programs and Features". To do so, you should go to "Product Details" page of your setup project and either uncheck the "Register with Windows Installer" option or check the "Do not show in list" option.
Otherwise, if you do want to launch an application on setup change mode, then you should try to configure this launch on a button push of your installed dialogs. For instance, when change operation is launched your setup package runs on maintenance mode and will display the dialogs under "Maintenance" group displayed in "Dialogs" page of your project. So, you can configure a custom action (i.e.
to launch your app file)
on a button pushed from one of those dialogs.
All the best,
Daniel