I forgot about those engines! The game resolution must be 84x48 in landscape or portrait so if the engine cannot scale/work in that requirement it would not be allowed.
I can only speak in Game Maker terms but your camera should be 84x48/48x84. You can leave the viewport at the required resolution or scale it for players so they are not looking at a tiny game window.
If you want to work in a lower resolution as an artistic choice it would have to be scaled up to the required resolution.
I hope that makes sense and answers your questions!