You can remove the controller using the Media Panel in InDesign (select None).
You can also set loop there.
Autoplay can be set in the Overlays panel.
You can try setting several properties at once in the output by attaching the following as a .js file in the Resources section of the in5 dialog:
The success of that code may depend on whether or not it executes before the media player elements are initialized (I haven't tested it).