Most door rattles and vibrations can be mitigated with DIY methods. Unfortunately most techs are instructed to "replace", which often doesn't solve problems when the item they are replacing is of a defective design.
I took it upon myself to silence my 2017 MQB Golf's doors (which weren't rattling at all, but I had to remove them for other reasons and wanted to be proactive regarding rattles).
The door panels themselves are made from many different parts that are either "plastic melt riveted" together, stapled together, snap-fit together, or glued together. Sometimes all of the above. They are made from a combination of different plastics and in the case of the Golf (not sure of the MQB Jetta) even fiber board.
I did a few things:
First, I applied sound-deadener on the bare door frame to deaden panel resonance.
Second, on the back side of the door panel, I smeared clear RTV silicone along all the plastic seams and junctions that were melt-riveted together. Those melt-rivet seams are a common source of audible vibration.
Third, I applied 6mm adhesive backed foam sound insulation to the back side of the door panels. I cut many different pieces designed to fit into all the irregular cavities of the door panel and cover about 85% of the panel area overall.
Fourth, I examined ALL the wiring harnesses that run along the door between the door frame and door panel. I supplemented the factory fabric-tape wrapping with additional Tesa tape (the same stuff German OEMs use) and made sure that all the panel clips holding the wiring in place were secure and not able to rattle.
Fifth, while I had the door panels off, I ran a bead of RTV silicone around each speaker frame, where it mates to the door frame. Those speaker frames are NOTORIOUS for leaking water into the cabin.
Sixth, I ran a bead of silicone RTV around the pop-out plastic panel in the door frame that provides access to the window mechanism. It's a large-ish plastic panel and it can be a source of vibration. VW did not design it to fit too tight. With the silicone, if the panel has to be removed for any reason, it's not difficult. RTV does not bind very strongly to surfaces but does an amazing job of damping vibrations.
Now my doors are SILENT. I have the VW Helix amp/subwoofer upgrade and no matter how much bass is pumping through the speakers, my doors are rattle-free and vibration-free. When the doors close they sound like a muffled bank vault door shutting.
I now also rest assured that my doors will not leak water into the car.
There is no way in hell you can expect a dealer to take a holistic approach like this to rid a car of rattles. These are technically modification, which dealers do not do. They only replace.
VW has made a LOT of cost-cutting shortcuts on their MQB cars post-dieselgate. Those rattles are probably one manifestation of those cost-cutting measures. Audis do not have these problems and if you dismantle their door panels, you will see a lot of the above approaches incorporated into the actual design (in the form of more sound insulation, primarily).
Good luck!
