On a completely unrelated note, you can simplify your WixSourceGenerated if you use Wix# XML Fluent extensions:
And starting with the next release I enabled support for AttributeDefinition in LicenseBootstrapperApplication. Thus you will be able to set the attribute even without using WixSourceGenerated:
project.WixSourceGenerated += (document) =>
{
document.Select("Wix/Bundle")
.FindSingle("WixStandardBootstrapperApplication")
.SetAttribute("ThemeFile", @"res\RtfLargeTheme.xml");
}Application = new LicenseBootstrapperApplication() { LicensePath = @"res\license.rtf", LogoFile = @"res\Logo.png", AttributesDefinition = @"ThemeFile=res\RtfLargeTheme.xml" };