RuntimeSection of the config file update at runtime using this code:    
private void ModifyRuntimeAppConfig()
{
  XmlDocument modifiedRuntimeSection = GetResource("Framework35Rebinding");
  if(modifiedRuntimeSection != null)
  {
    Configuration config = ConfigurationManager.OpenExeConfiguration(ConfigurationUserLevel.None);
    ConfigurationSection assemblyBindingSection = config.Sections["runtime"];
    assemblyBindingSection.SectionInformation.SetRawXml(modifiedRuntimeSection.InnerXml);
    config.Save(ConfigurationSaveMode.Modified);
    ConfigurationManager.RefreshSection("runtime");
  }
}
with Framework35Rebinding containing:
<runtime>
  <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
    <dependentAssembly>
      <assemblyIdentity name="Microsoft.Build.Framework" publicKeyToken="b03f5f7f11d50a3a" culture="neutral"/>
      <bindingRedirect oldVersion="0.0.0.0-99.9.9.9" newVersion="3.5.0.0"/>
    </dependentAssembly>
    <dependentAssembly>
      <assemblyIdentity name="Microsoft.CompactFramework.Build.Tasks" publicKeyToken="b03f5f7f11d50a3a" culture="neutral"/>
      <bindingRedirect oldVersion="0.0.0.0-99.9.9.9" newVersion="9.0.0.0"/>
    </dependentAssembly>
  </assemblyBinding>
</runtime>
and an app.config containing (before the execution of the program):
<?xml version="1.0"?>
<configuration>
  <startup>
    <supportedRuntime version="v2.0.50727"/>
  </startup>
  <runtime>
  </runtime>
</configuration>
Nevertheless it doesn't work for that I wanna do because assemblyBinding is only read at startup of the application whereas the RefreshSection("runtime")