In my managed bootstrapper, I\'m packing Net framework 4.5.1 and VC Redistributable as follows:
The Burn engine will register the bundle in Add/Remove Programs as soon as any part of the bundle is installed. The .NET prerequisite package is part of the bundle, so when the MBAPrereq BootstrapperApplication installs .NET, the bundle is registered in Add/Remove Programs. There is no way to modify this behavior of the Burn engine in your Bundle or BA. A potential feature request could be for Burn to only register the bundle after a non-Permanent package has been installed. Feature requests should be filed at http://wixtoolset.org/issues.
Today, you could try to workaround this issue by putting logic in your BA where it automatically uninstalls itself before calling Engine::Exit if it detects this scenario.