Since they are using OSX as the model, presumably, if they ever get to a release stage, they will be able to launch X11 from within Arix, just like you launch X11 from within OS X.
Similarly OS X has Carbon, which links back to the pre-OS X days and Cocoa, the NeXT framework that has just about buried Carbon.
So presumably Arix will contain a Carbon equivalent that will support old Amiga APIs and a Cocoa based on some new framework. Now Apple had thousands of full time programmers to take on the task, Arix has a couple part time hobbyists, so we'll just have to wait and see wether they can deliver a champagne OS on a water budget...