AME still renders the comps exactly as you have them set up. The render settings in the render Cue don't matter, but if you have a layer set to draft quality or motion blur turned off they will not render.
When rendering After Effects comps in AME, the rule of thumb is WYSIWYG. Whatever the Comp panel shows is what AME will render.
The exception to this is the viewer controls at the bottom of the Comp panel: resolution, grids/guides, channels, etc. Those only affect how you view the comp, they don't affect the content of your comp, which is what AME cares about.
In other words, AME will render your comp the way it is set up in the Timeline panel.