have following working implementation:

Project Name MyBa (Visual C# Class Library)

Class1.cs: (additional references were afaik BootstrapperCode + windows forms)
using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using Microsoft.Tools.WindowsInstallerXml.Bootstrapper;
using System.Windows.Forms;


namespace MyBA
{
    public class TestBA : BootstrapperApplication
    {
        protected override void Run()
        {
            MessageBox.Show("My BA is running");
            this.Engine.Quit(0);
        }
    }
}


TestBA.BootstrapperCore.config:
<?xml version="1.0" encoding="utf-8" ?>
<configuration>
    <configSections>
        <sectionGroup name="wix.bootstrapper"
type="Microsoft.Tools.WindowsInstallerXml.Bootstrapper.BootstrapperSectionGroup,
BootstrapperCore">
            <section name="host"
type="Microsoft.Tools.WindowsInstallerXml.Bootstrapper.HostSection,
BootstrapperCore" />
        </sectionGroup>
    </configSections>
    <startup useLegacyV2RuntimeActivationPolicy="true">
        <supportedRuntime version="v4.0" />
        <!-- supportedRuntime version="v2.0.50727" / -->
    </startup>
    <wix.bootstrapper>
        <host assemblyName="MyBA">
            <supportedFramework version="v4\Full" />
            <supportedFramework version="v4\Client" />
        </host>
    </wix.bootstrapper>
</configuration>



AssemblyInfo.cs (interesting parts)
using System.Reflection;
using System.Runtime.CompilerServices;
using System.Runtime.InteropServices;
using Microsoft.Tools.WindowsInstallerXml.Bootstrapper;
using MyBA;
...
[assembly: BootstrapperApplication(typeof(TestBA))]


Bundle.wxs (including WiXBalExtenstion):

<?xml version="1.0" encoding="UTF-8"?>
<Wix xmlns="http://schemas.microsoft.com/wix/2006/wi";>
  <Bundle Name="Bootstrapper3" Version="1.0.0.0"
Manufacturer="Bootstrapper3" UpgradeCode="aUpgradeCode">


    <BootstrapperApplicationRef Id='ManagedBootstrapperApplicationHost'>
      <Payload SourceFile='..\MyBA\bin\debug\MyBA.dll' />
      <Payload Name='BootstrapperCore.config'
SourceFile='..\MyBA\TestBA.BootstrapperCore.config' />
    </BootstrapperApplicationRef>

    <Chain>
      <PackageGroupRef Id='Netfx4Full' />

      <MsiPackage ...
/>
    </Chain>
  </Bundle>
</Wix>

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