Wix#
The easiest way to handle this problem is to indicate what .NET you want to be installed. The following change will make light happy:
SilentBootstrapperApplication is built using WiX ManagedBootstrapperApplicationHost bootstrapper app which is a WiX managed module. Thus WiX introduces .NET package dependency for both ManagedBootstrapperApplicationHost and WixStandardBootstrapperApplication application types expressed via WixMbaPrereqPackageId WiX variable referencing the specific .NET package to be installed. The easiest way to handle this problem is to indicate what .NET you want to be installed. The following change will make light happy:
var bootstrapper = new Bundle("MyProject", new PackageGroupRef("NetFx40Web"), new MsiPackage(msiFile)) ...