The verbose "Running Installer in Isolated Environment" will happen either you have some wrong configurations or your app will pop up other windows when you run the command setup.exe /s. In my understanding, it may be the latter, you can try to
use the setup.exe /s command to observe whether your app will show other windows when the app is installing. If it shows, you should find a way to make your app install silently by configuring some parameters in the command.
By the way, could you tell me how do you create your setup.exe file? We will try to help you with this issue.
Besides, here is a similar example thread, you can also have a reference.