Well if it's an original top and thus 3 years old, and since these tops do have a normal life expectancy, the offer to split the cost with you seems reasonably fair. Chances are you'd be replacing the entire top on your own dime in another 3 years anyway. Also, when the top gets replaced, they can take steps to make sure this doesn't happen again.
I checked all the Tecnical Service Bulletins for the Z4 convertible top and there is no mention of this problem.
Maybe if it goes well with your car, you could order a black top.