Yes the engine is changing the aerodynamics of the car. When it is stationary only the wind blows over it, when they open the throttle the car starts moving and the car cuts though the air, and that creates downforce. Also, albeit nitpicking, the engine heats up the engine cover and that changes the airflow over that part of the car, the engine exhaust also blows towards the rear of the car, no matter how you angle it, and that changes the aerodynamics of the car.
They are not wasting fuel, they are using it to go faster. That is the point of F1. They all end up where they started anyway, it is just about covering as much ground as quickly as possible, and to do that you burn fuel. It is all just wasted.
Sport is wasteful, but that is a part of the fun. To do something, just for the purpose of doing it.
The wheels also changes the aerodynamics of the car, when they are moving and when they are not. It is a movable aerodynamic device. The whole car is a movable aerodynamic device. That is the point of downforce.
FIA had their chance to change things at the end of last year, they didn’t. Bad luck for them. They shouldn’t punish the teams because they messed up.
I don’t think mid season rule changes are fair to anyone, it is just not what the sport is about. It is about designing a car by the rule book and then racing it for a year while updating it, still by the same rule book. They shouldn’t change things in the middle of the season. That will punish the people who have been using the rules to their advantage, and give the people who have been playing safe an advantage. That is just not what F1 is about. It is about being creative, daring to go beyond the known limits and trying things out. Not about designing the cars like the FIA want them to.