I'd like to
remove my roof rails to improve fuel milage (I've done it before, I can do it again), however, I'd like to be able to put on a roof
rack from time to time to carry a boat or cargo box.
Does anyone know if there is a roof rack option that affixes directly to the car (rain gutters?) Preferably one that comes on-and-off in just a few minutes?
Should I maybe look at the roof rack options for the Jetta sedans or hatchback?
Because we have had a MkV sedan (since 2006) with a Thule rack (both square bar and aeroblade bars, using the same Fit Kit) which we used to tote Thule Roof Top boxes thousands of miles, and we now a 2013 JSW, I know a little bit about what you're asking.
I can tell you the JSW does NOT have the peg holes for the front bar side clamps for a typical MkV (Thule Kit 1597) or the MkVI (Thule Kit 1618). Our MKV Sedan had black rubber screw plugs you removed with a very small allen wrench, doing this created a female receptacle for a peg on the rack side arm which allowed the front bar to stay fixed in place. If you look at the Thule 1618 fit kit instructions, you'll see the MkVI used the same concept as the MkV (fit kit 1597), the front bar side brackets are held in place with a steel dowel that fits up into a hole in the top of the door frame which our 2013 Wagon doesn't have. (I presume your wagon does not have these either)
That being said, my side clamps for the Thule fit kit for my Corrado do not have pegs, so Thule didn't always use pegs to hold the side clamp brackets in place...
If you acquired a MKVI fit kit for a sedan, at a minimum, you'd have to drill out that peg from the Thule Part Number 1149 clamp brackets. (part number reference comes from the Fit Kit PDF).
For those who stumble upon this thread, here's a site with many of the old fit kit instruction sets:
https://roofracks.co.uk/_pdf/
Here's a link to a PDF of the Thule 2012 fit kit guide which included fit kits for many of the Thule 400 XT risers (which seem to be discontinued, but are available from practically anyone selling a used Thule rack):
http://partprice.com.ua/media/files/file/thule_guide.pdf