The list of formats on the panel is not highlighted as active when creating a new scene through the API because the UI reads those values from specific scene properties, which are empty or set to 1,1.
However, you can override them manually using the following code:
const scene = engine.scene.get();
engine.block.setString(scene, "scene/pageFormatId", "<id>");
engine.block.setFloat(scene, "scene/pageDimensions/width", 1920);
engine.block.setFloat(scene, "scene/pageDimensions/height", 1080)