Does this simply mean it goes in front or does it have to go on the front passenger side? I have had some whistling and was checking out the dealer install and noticed that the sticker was on the front driver side - does that matter?

Also is the rubber strip that everyone talks about on top of the crossbars or are they something else.

 

The front one has three nubs on the bottom to reduce noise. I believe that decal should be on passenger side.

 

Would being mounted on the wrong side make a difference with whistling?

 

Probably not, but reversing the cross beams would make a difference. The reason you are placing the container on the passenger side is for easy access. Personally, I centered mine because it looks better.