How does Windows Installer close an application during uninstall?

When uninstalling my application, it attempts to stop it if it's running:

Sadly, the automatically closing doesn't really work and it displays this error:

My applications disappear, the windows, the tray bar icon, they are all gone. But I can still see them in the process list.

I'm guessing Windows sends a signal to the applications to exit gracefully and the UI does so, but there's some lingering thread preventing the processes from terminating.

How does Windows Installer close an application during uninstall?

Once I know this I want to simulate it while debugging my app to see what's going on. Is this a sound plan?

Since Windows Vista, Windows Installer will leverage the Restart Manager to identify, close, and restart applications. Microsoft's documentation on Using Restart Manager, and in particular Using Restart Manager with a Primary Installer should be a solid starting point for implementing a test harness. Your applications and services should instead follow the Guidelines for Applications and Services.

The Guidelines for Applications discuss the messages sent to your application by the restart manager; services are restarted through the service control manager. In theory you could simulate the restart manager at that level, but I suspect you'd be better served by invoking the real thing, registering a carefully chosen list of resources to target just your application, if possible.