OK. It seems that the windowless managed BA is the way of achieving silent Bootstrapper. Apparently Burn will bootstrap .NET first if custom BA is defined.
There is an interesting discussion on the matter: http://windows-installer-xml-wix-toolset.687559.n2.nabble.com/Burn-without-UI-td7239834.html
There is an interesting discussion on the matter: http://windows-installer-xml-wix-toolset.687559.n2.nabble.com/Burn-without-UI-td7239834.html