I think the best answer is for your case is like this: think about AxRuntime like a set of additional libraries that you can use in your Linux application. If you application uses SDL2, it will use Linux-side SDL2 which will open a Linux window that is not controlled by Intuition. However in the same application you can use Dos calls to read files, or show Intuition requesters or use Datatypes. This will work together with Linux-side SDL2. Of course this application won't be available under AROS, because we are missing SDL2 port ATM.