The native dialogs and alert views are determined by the operating system and can not be modified. You can leverage modals and other UI element via web frameworks such as Material Design for Bootstrap.
the native 1 in chrome and web view will be the native input base on the android version, but XDK build will always get the Android 1.6 theme
and there is no way to modified the manifest like phonegap to modified it, waited half year plus but still no update from your side
There have been some attempts to modify this using a simple plugin. Search the forum, I believe someone managed to modify the default theme using this technique. The next release of the XDK normalizes the theme used by the custom Debug module and the build system so they are the same.