As they say with many British low volume cars, "they all do that sir". It is usually a very minor rub (like yours), maybe a bit more if the drive belt has been on the loose side. On my M3W I put a thin piece of sheet aluminium in the area of the rub with a pair of Jubilee clips either side to hold it in place. It helps protect the chassis but also reduces the clearances slightly, so more rub. The same bit of aluminium has been on there for thousands of miles.
No signs of damage to the belt and not a big problem to my mind. Your guess about the cause is about right I think. The designed lack of clearance maybe another consequence of the change to a heavier duty belt drive in the very early M3W production, as are the tyre sidewall and shock absorber clearances I suspect..
