Can't see why they would. How are they to know if the car was fitted with or without run flats? You can spec a BMW without run flats now. The M versions no longer come with Run flats so I assume this is the assumption that all BMWs come with run flats which is incorrect. When I had my first car, a mini if you went for 15 inch alloys standard tyres with a compressor and gunk then 16 inch alloys fitted with run flats but if you bought wheels from BMW after you bought the car you could state the tyre to be fitted, just like any other garage.
So no, there should be no fuss made