If your aiding an attack while the enemy has lesser cover does it matter? I recently learned making a trip attack when the enemy has lesser cover doesn't matter, you don't suffer any penalties because your targeting their reflex save, but what happens if your aiding an attack and enemy has lesser cover?
Aid rules do not have a sharp definition to give a RAW answer to questions like that from.
The penalties that apply to an aid check are whatever seems relevant to the GM, based on the situation and the description of what you are trying to do as an aid action.
This may include cover sometimes, but not others.