Here are all of the differences. What does ISU do to include these files? I want to accomplish it with VS Publish without getting into an arms race with JS files deep in the folder structure.
Export Logic has debug=false in web config.
Export Logic has, but VS Publish does not:
/FileUploader/js and images
/ThirdParty/js and txt and css
ExportLogic does, but shouldn't, include /PublishProfiles and Web.Debug.config and Web.Release.config.