vw beetle radio need tech help

my wife has a 2000 beetle 1.8 turbo. the factory radio went bad so we had it replaced with an aftermarket alpine head unit. now the check engine light is on and the car won't pass emissions inspection. the dealer says the radio has to be removed and replaced by the original for complete diagnostic. am i the only one who thinks that is the dumbest thing i've ever heard. does anyone know a fix except replacing the radio with a stock one every year before emissions inspection. please help. thanks.:disappoin