I can't really see how this is different from a native-code based device, especially one which is actually following good practice by not trusting what's in fla

I can't really see how this is different from a native-code based device, especially one which is actually following good practice by not trusting what's in flash. Every stage of the boot chain still has to validate the next - there's just one more layer on top where the application is the runtime VM and it has to validate sub-applications / managed code.