Rectangle holes on roof rails? For cross bars right?
 

hello - noticed two rectangle holes on each side of the roof rails. I assume these are for cross bars? Manual doesn't state exactly how to remove,etc?

Does this mean that the Audi cross bars, or Thule, must be mounted at those locations only? Like, I cannot shorter or widen the distance between cross bars?

Correct. I haven't seen any that could be attached outside the designated mounting locations. The design of the rails makes it difficult to keep the bars secured.