I agree with posters on rust not affecting the ability magnetic field. However, lets review what rust is. It's the break down of steel/iron due moisture/water. This is why when the rust is cleaned away, the parts shows as pitted. The breakdown is composed of fine particles of decomposing steel/iron, which does affect the engines ability to start or make a spark. The accumulation of rust/fine particles can easily be enough, reducing the air gap to the point grounding out the coil, just like the ground wire would. It seems odd to me that many engine manufacturers have modified flywheels so the magnet portion is raised, in some cases quite a lot (Kohler CH Series). Just my two cents and 40+ years repairing!
Remember way back in high school when they tried to teach you the fundamential principles that described the behaviour of everything in the universe, people including.
All bodies will try to revert to their lowest energy state, they are not degrading, deteriorating or doing anything other than reverting to the energy level where they are in equlibrium with their surrounding
Thus steel which was made from rust which is it's natural state in the enviroment will give up the energy used to raise its energy level from rut to steel and revert to rust it's natural state.
And the same goes for every metal, every piece of wood and even plastic.
The only real difference is the rate of the reversion and that largely depends upon the strength of the oxide, sulphide, chloride, hydroxide, iodide etc etc that forms on the surface