While it is true that in 6.1 you can create this folder and in 6.2 you "can't", I do not understand the reason to do this to begin with.
You shouldn't need to create this folder because you can see that the LibInclude folder already exists in the application's folder structure: iphone\native\XtifyLib\CustomInbox\LibInclude.
Are you perhaps trying to add additional files to this folder for later use?
The scenario is not clear enough.
IF what you want is to add there files for later use, then also note that it is not enough to just place files there, because after building and opening the Xcode project, those files will not be linked - you will still need to select "Add files..." (in Xcode) and add the files so that they will be known to the project.
Additionally, you may want to store your additional files(?) not in the iphone\native folder, but in the iphone\nativeResources folder.
Simply recreate the folder structure within: iphone\nativeResources\XtifyLib\CustomInbox\LibInclude
Then you can save in your SCM the nativeResources folder instead of the native folder.
On the next build, the files from the nativeResources folder will be copied into the native folder respectively.
Note that you will still need to link the files when the project is later opened in Xcode.
It will help if you will explain the full scenario