On Start Stop Engines the Engine stops at the exact same place each time, it is where the minimum amount of energy is required to re-start. At this point in the Flywheel and Starter where the components mesh only are hardened for long life.

 

Quite clever.

Flywheel isn't really affected by engine start-up, especially when it is on working temperature. Starter is designed for this job and none of the issues are noted on such cars, even long after usual working period. I live in a country where majority of cars are imported, with huge mileage, and most of them still work with original engine, flywheel and starter. Probably only battery has to be replaced after 6-7 or more years of usage. 

 

In other words, I wouldn't worry about this system unless it annoys you. It does save some fuel and engine wearing, but it's up to you how you manage it. It did annoy me on diesel, but on this nice petrol it does not. I don't even know if the engine is working or not on idle if a music is on, or skyroof is open.