You could always build your own rack to go with your home-made boat. I made these prototype A-frames for my Ranger and they have been working really well for the past two years; I'm getting ready to build a more refined version in the near future.

I did the same, custom J racks for my SOF and WD12.  Had the advantage of being able to elevate the aft end to be able to open the rear hatch of the car (Volvo XC70). 

I keep a tonneau cover on my truck, and this truck is my first non-work truck since driving pick ups since 1970.  I have never liked fixed racks on a truck, even though at times I had to have them, and am definetly going to use the "T" bar in the receiver and a single roof rack. I  guess I should re-define the question to round bars compared to square bars on a rack.   

yeah, they can look a little... I only have mine on when I going boating. 

Facing the prospect of a pick up as my next vehicle, I did find this as an intriguing option:

http://www.etrailer.com/Hitch-Cargo-Carrier/Darby/DTA944.html

I have Yakima rollers on the rear and cradles in the front mounted to Adarack truck racks. These racks have 1 inch square bars. I didn't like the adapters provided by Yakima, so just fabricated square pieces of plywood, drilled to the Yakima bolt pattern and used as a lower bracket. All bolted together with SS bolts. Very sturdy. Both the Yakima rollers and cradles work well with my CH18, though the Thule cradle pads might work better for flat surfaced hulls on S&G type hulls. I went through the same thought process on the round vs square and opted for square for exactly the reason you mention. 

I should add that I also have a receiver rack and it is very wobbly unless I secure it with straps. I'm not familiar with the Thule system so they may already provide something for this, but either way, you've got a big lever arm and a not-so-precise receiver(dimension wise) that you will need to control with straps or cables. 

How did you find this racks and at which amount? I searched for it I get best deal on all marine parts. If you also interested then you can visit here .

I went for the Yakima Drydock with one Q tower rack.  I am using Mako Aero saddles and Hully Rollers.  They don't really seem to be a problem turning on the bars, and if they do I will add a couple of wraps of Rescue tape to add friction to prevent them from turning.  Problem is the distance between the roof rack and the receiver rack. At 9' between racks, my SW Sport Hybrid JUST makes it and sit properly on the rollers and the saddle.  My Plastic boat will work if deck down.  My wife's plastic boat is too short and will only catch about a foot of the bow and stern in the J-bars.  I will need to add another rack on the roof.  Will work perfectly when I build a Petrel, and will need to build my wife something longer,with a long cockpit to allow her to sit in the boat, she has mobility issues, and has a leg that doesn't bend.