They'll try and avoid fixing it, under warranty. However if the warranty was up and you were footing they bill they'd tell you there was something wrong. Warranty work doesn't pay as well as retail shop work does, so they sometimes pick and choose what they want to do. Pulling a tranny under warranty isn't one of the easier more profitable jobs especially for a busy dealership, they tend to go to the higher paying more profitable jobs if possible. OTOH if the rep tells them to drop the tranny and do the job, they have to.
Keep in mind some clutch chatter is considered normal, and might not occur all the time, now if the rear main seal were leaking and it was obvious it would be cut and dry. Check for oil leaks, you never know. Last thoughts, chatter and TOB noise are two totally different animals. Some MTs make a roll over noise, that is considered normal too. Good luck!