I think your tire place was trying to take you for a ride so to speak. There are a lot of places that seem to be really stupid about run-flats and apparently think the consumers who has them are also dumb. Run-flats are just tires with enhanced sidewalls. Some cars have a wireless TPMS, MINIs do not. The flat-tire indicator uses the ABS system to monitor the wheels for a difference in rotation. It does not know if the tire has lost 5psi in pressure. In order for that system to work properly you need to reset the Flat Tire monitor everytime you top off the pressure so the system can recalibrate itself. If your tire light came on after miles (3 miles or 50 miles, you didn't say), that might be how long the tire took to deform enough to set off the monitor at its current calibration level. I can't say that I've experienced how this works yet.

That and the non-S coopers have donuts because they come with 15" regular tires normally. The sport package gets you run-flats, but why remove the donut if it's part of the package anyway? That and it makes "upgrading" to standard tires easier if you have a spare, since you get that peace of mind.