I have looked into this a lot, I made the mistake of thinking that as long as I had the correct engine I could get a dealer installed hitch later. Of course what I found was that yes I could have a dealer installed hitch but only 2,000 lbs. When I went in I asked the service manager to show me the difference in the vehicles with regard to the factory installed hitch, he spent some time with the parts guy and could not, no transmission cooler or other parts on the vehicle with the factory hitch but not on my SE with VR6 and 4Motion. He came to the conclusion that there must not be a difference other than the hitch itself so I asked him to get the part number off of the 5,000 hitch and order me one. He did it but it was a no go. VW told him that Volkswagen put additional chassis bracing in the vehicles equipped with a 5,000 lb hitch from the factory and that dealerships are only allowed to install the 2,000 lbs. hitch. Had I known this I never would have bought the vehicle.
I have seen older vehicles with hitch systems that had a U shaped bracket that went around a frame member before a hitch was installed it is probably something like that. It can't be much though. Just look at the price. The factory tow option cost MSRP $ 550 when you subtract the cost of the hitch itself from the $550 you are left with about $ 165. You know you are not getting much from the factory they charge $149 for a set of mojo floor mats so just how much are you getting for $165, nothing major like transmission coolers and such.
What I have not found out about is what exactly is this additional factory bracing consists of and why can't it be added at the dealer. I want to know the answer. Normally I would just go find a wrecked Atlas at a junk yard with a 5K hitch and buy the hitch off of it and while doing so take a look myself to see what is different. But I can see VW's reaction, they would probably flag you on their server and if you ever had a warranty problem deny coverage so I will just get the 2K hitch and it will act as a reminder never to buy VW again. I don't like being tricked and their marketing did just that, trick me.
You go on a VW lot now and look for a SE with VR6 that does not have the factory hitch, you will have a hard time finding it, this because VW found out they were screwing over their customers who wanted to put a hitch on later and it was pissing them off. I know I will never buy another VW and I have been a VW person my whole life.