Try to think of your new deal and old deal separately. You have a vehicle that has X miles with a current payoff of Y. The absolute most you should ‘pay’ to the dealer in your next deal is the difference between those two numbers. Meaning hypothetically your payoff is $12k and the car is worth $9K wholesale. So owing $3k currently (apply whatever the real numbers are) is your worst case scenario. Your other option is as you suggested pay the remaining payments and pay the mileage penalty.
Make sure you have a really good grasp of both sides of the deal. You could for instance call a couple other dealers and tell them you are shopping a zero down Jetta deal and get quotes. Then do some addition on your own and add in the negative equity so you know you’re not getting screwed on the turn-in.
Also, forget the whole “I’ve already bought two cars here, so they’ll take care of me.” In reality, the GM is probably looking up the gross on your last deal and trying to beat it. You being loyal will cost you money, not save money. You want dealers to slit each other’s throats - not yours.