I do not understand your noise description, but I too am interested in the source of noises heard while driving an 06 TDI. I do know that failing to rotate tires can affect the tires tread shapes such that road noise from them becomes different. I also know that some cars transmit noise to the cabin differently from other cars. I once had a 1995 Ford Windstar that was much quieter than its replacement, a 2005 Honda Odyssey. My daughter's 2000 Toyota Camry has less road noise than my 2006 TDI Jetta.
This is an interesting question to me. I recently completed an overhaul of my 06 TDI manual Jetta that included: New CV joints, one new front wheel bearing, new brake rotors and pads front and back, new thermostat, new cam and lifters, new timing belt, new water pump, new oil pump, new door lock and something else I can't remember right now. Since doing so, I have been paying a lot of attention to the sounds I hear from the car while driving, and speed related noises, in addition to engine related noises.
I hear various speed and road surface dependent hums and growls, the sources of which I am uncertain, and due to uncertain memories, do not recall whether these noises were previously there or not. I am wondering whether or not there are rubber containing or other suspension parts, the performance of which degrades with age such that their replacement would make appreciably significant interior road noise reduction worthwhile. As such, I would appreciate hearing from any of our group that has found specific part replacements to have had any noticeable impact on interior road noise in this model VW.