issues with the water trough back of the moonroof and rattleing

What is your question?

I was told by the dealer that the rattling was seperate from the water trough being cracked but after reading online it seems that it is all linked together. They want to charge me $339 just to replace the water trough but not the issue with the rattleing. So, my question is, if it is all linked together..is it possible that for $339 it will all be taken care of or is it that they are trying to sucker me into paying twice for the same issue???? Does the water trough being replaced take the rattleing away, and keep water out of my car or do other parts need to replaced also?