It's kind of hard to read anything specific into the logo of any one of the VW group companies (VW, Audi, Seat, Skoda, Bentley, etc.) appearing on a part. It could be that the same part is used on an Audi car, or, it could be that one of Audi's subcontractors manufactures that part specifically for the Phaeton. I've seen some parts in my Phaeton that have Seat or Skoda logos on them, even though it is obvious that the part could never be used in a Seat or a Skoda, because those products are much smaller vehicles.
Maybe a better way to look at the question, from a parts point of view, is that any VW AG product could have a part on it that is made by any subcontractor to the group, or, the part could also be used on any other carline of the group. For example, the rear spoiler controller on a Bentley Continental GT has a VW logo on it, because it is (essentially) the same thing as the rear spoiler controller for the New Beetle Turbo. The functionality might be different, though, because the GT has a higher top speed than the NB Turbo - at least, outside of NAR, anyway.