intelxdk.config.xml is no longer necessary to create for building Cordova apps in newer versions of Intel XDK, the Cordova config.xml files are automatcally generated for each platform in the Intel XDK project settings UI. The basic config, icon/splashscreens and plugins are all options in IntelXDK project page that have to be configured, which in turn will generate the config.xml. For platform specific preferences you will have to create a intelxdk.config.additions.xml file with just the preferences. All the preferences available for Cordova 3.5 are in the intelxdk.config.additions.xml file, which can be modified to remove the ones that are not applicable.
All the preferences available for Cordova 3.5 are in the intelxdk.config.additions.xml file, which can be modified to remove the ones that are not applicable. Use this file in Intel XDK project and also refer to the project settings page to configure icon/splashscreens and plugins for Cordova build.
Documentation