Use config defaults to default themes to atom-dark-*

src/app/atom.coffee

@@ -111,7 +111,7 @@ _.extend atom,
     fsUtils.base(path) for path in @getAvailablePackagePaths()
 
   loadThemes: ->
-    themeNames = config.get("core.themes") ? ['atom-dark-ui', 'atom-dark-syntax']
+    themeNames = config.get("core.themes")
     themeNames = [themeNames] unless _.isArray(themeNames)
     @loadTheme(themeName) for themeName in themeNames
     @loadUserStylesheet()

src/app/root-view.coffee

@@ -23,6 +23,7 @@ class RootView extends View
   @configDefaults:
     ignoredNames: [".git", ".svn", ".DS_Store"]
     disabledPackages: []
+    themes: ['atom-dark-ui', 'atom-dark-syntax']
 
   ###
   # Internal: