Experimentally, I simply copied WixBA project from WiX 3.7 source, replaced the reference from core.csproj to BootstrapperCore and tried to use it with my own Bundle which is working fine with my own Manged Bootstrapper. It built fine. But strangely, when I tried to run it, it showed me the dialog to install .NET framework. And I already have .NET framework 4.5 installed. I even tried with changing the WixBA's Targetframework to 4.5, but it resulted in the same thing.
Why is that so? Is there any security technique used, so that no other Bundle can be used with it? If yes, what is the explanation?