All the ones I have experience of are similar. The Yakima one do not fit the car properly and need pretty much dismantling every time they are fitted. I sent the ones I ordered back. I would use VW original or find somewhere that has Thule that you can see fitted to the car before buying. There is barely any price difference between VW and Thule.
I have VW bars with Thule bike carriers. The Mont Blanc Barracuda bike carriers also fit. You have to be a bit careful with some of the wider aero bars as some accessories will not fit.
The VW 3 door roof bars are the same as 5 door with the exception of the angled section that grips in the window recess being about 20mm shorter. 3 door will a 5 door but the other way round needs the bracket trimming if you were to go that way.
Personally I would only do that if I could get some cheap enough second hand!