The DMF is a wear item at this point. Be it a standard or automatic, they have issues, and VW keeps updating them. I don't know if the newest version is reliable or not, but the old ones certainly have a problem.
Mine started making noise at about (I'm guessing) 100,000 miles. I am now at 132,000 and it is still making about the same noise. I will probably have to change it soon.
I got a quote of $1,250 from an independent, and something like $2,200 from VW.
The transmissions are generally good. Some people have had issues with the mechatronics unit, but I think that has been taken care of. I don't know the lifespan of the clutches, but it should be good. Proper oil change intervals are supposed to be important, especially the first one. Someone here (Oilhammer?) saw a customer's car that had over 100,000 miles on the fluid, and the trans was still working, IIRC.
The one thing that I have had go bad on my car was the exhaust flap. It's been replaced twice now (under warranty). I expect it to go bad one more time before I turn the car in. I am guessing they lasted 50-60,000 miles.
The other is the pressure sensor for the DPF, and they don't warranty that as an emission component, so it is 3/36.
In my non-professional opinion, the weak links, or potential problem areas are: DMF, mechatronic unit, and clutches. I have never heard of anything else going bad in the transmissions. To be honest, I personally don't expect you to have problems with the mech. unit or the clutches.
I don't think the extended warranty is going to do you any good. I believe they are from the date of the fix, and are supposedly only going to be 4 years/48,000 miles. The HPFP is already warrantied to 120,000 miles. The DPF is 80,000 IIRC. You might get a little more on that, with the extension.
