We had a local vinyl graphics company do some black 'humbug' over-roof twin stripes on our (now long gone) '07 plate white Mini One. Looked great, stood up to 4+ years of car washes without any sign of deterioration or peeling. Cant remember what they cost, but wasn't a lot. Knowing me would have been cheaper than dealer option.
Our new MINI was pre-built with no stripes and had the dealer quote up for some stripes - as others have said it goes over the clearcoat.
Ended up going independent as the dealer quoted a pretty penny to have them done, I can highly recommend Printworx in Oxfordshire - price was a 1/4 that of the dealer and they did a fantastic job. They have a website and are on Facebook too - can highly recommend them if anyone is looking to have some aftermarket stripes!