Hi Jiri, 

I just managed the task you describe (albeit wit .Net 4.5.2.) with the
follwing setup.
 
--------------------------- 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" sku=".NETFramework,Version=v4.5"/>
    </startup>
    <wix.bootstrapper>
        <host assemblyName="CustomBA" />
    </wix.bootstrapper>
</configuration>
----------------------------------------------------------------------------------------------------------

--------------------------- bundle.wxs
-------------------------------------------------
<?xml version="1.0" encoding="UTF-8"?>
<Wix xmlns="http://schemas.microsoft.com/wix/2006/wi";>
  <Bundle Name="MyBootstrapper" Version="1.0.0.0" Manufacturer="WiX Tests"
UpgradeCode="416b6bbf-2beb-4187-9f83-cdb764db2840">
        <BootstrapperApplicationRef Id="ManagedBootstrapperApplicationHost">
         
          <Payload SourceFile="$(var.CustomBA.TargetDir)CustomBA.dll" />
          <Payload
SourceFile="$(var.CustomBA.TargetDir)BootstrapperCore.config" />
          <Payload
SourceFile="$(var.CustomBA.TargetDir)Microsoft.Practices.Prism.dll" />
          
        </BootstrapperApplicationRef>

     
     <WixVariable Id="WixMbaPrereqPackageId" Value="NetFx452Web" />
     <WixVariable Id="WixMbaPrereqLicenseUrl"
Value="http://go.microsoft.com/fwlink/?LinkID=260867"; />
    
    <Chain DisableSystemRestore="yes">
      
      <PackageGroupRef Id="NetFx452Web"/>
      <MsiPackage SourceFile="$(var.MyInstaller.TargetPath)" />
    </Chain>
  </Bundle>
</Wix>
----------------------------------------------------------------------------------------------------------

Please note that BootstrapperCore.config enforces the use of .NET 4.5 for
the managed bootstrapper application by using the sku Attribute at Tag
supportedRuntime. The possible values for this attribute are stated here:
https://msdn.microsoft.com/en-us/library/w4atty68%28v=vs.110%29.aspx
I suppose this is the bit you are missing ?

Please note that the bundle.wxs explicitly sets variables
WixMbaPrereqPackageId and WixMbaPrereqLicenseUrl. This is necessary due to a
bug in WiX NetFx Extension described here:
http://wixtoolset.org/issues/4671/

In my Test of this Setup, i started with a clean win7 (having .NET 3.5). 

First, i manually installed .Net 40.

After that, I started the Installer. It first asks for .NET 4.5.2
intallation (with a native GUI provided by the WiX Libs) and only once the
installation is done, (replacing .net 4.0) the WPF GUI of the Installer
comes up - without asking for reboot.

Let me know if this works for you as well.



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