How do you handle packaging Win32 apps which auto-update? Since the app location of packaged apps is read-only I have issues with apps which auto-update on start-up. Unfortunately I can't disable auto-update on affected Win32 apps since this behaviour is baked into the code.
If you want to deploy the app via MSIX you definitely need to block the auto-update built-in support.
If you can't do it via the package binaries, you (sync with the corresponding team from your company) can try to block the URL accessed by the app to check for updates? Use Fiddler to find out what URL is your app using to check for updates and inform the corresponding team inside your company to block it.