This is not Adobe Air limitations. This also affect on any software. Android don't have such issues.
In your case - you can use external assest but only if you link external files as I said above. Adobe Air during compilation will rip source code from SWF and embed it to the app. Your server files can be used for app. Read this more details http://blogs.adobe.com/airodynamics/2013/03/08/external-hosting-of-secondary-swfs-for-air- apps-on-ios