I wouldn't do that. The "Magiver setup is probably much stronger than any Yakima setup. First off, the roof rack isn't for show. It holds 200 lbs. The "magiver" setup is probably good for well over 10 times that before failure. He did not choose hardware that is aesteticly pleasing, and I actually gave him an idea or two after the fact, but it is sound. If I was to do a similar mod, I would use a piece of brass or steel pipe instead of all the washers. Put a washer on top and below the pipe. I would then use a bolt of the correct length, not too long as is used. I'd use a lock washer (Star kind) between the nut and the Yakima plastic clamp (the clamp is the weakest part of the system) and leave 3/8" extra sticking out from the bottom. I'd also put thread lock on the screw so the nut wouldn't turn off or loosen. The plastic clamps would fail or the roof rack would be ripped off before the "magiver" failed and it would look nice. Wanna make it look nicer? Put a piece of black plastic wire crinkle cover over the pipe or paint the pipe black. Use black hardware and it would look stock. A good substitue for the pipe is a hockey puck. The rack would sit on the puck. It would act as a sound dampener and shock for the rack, and it is much stronger than needed. Just drill a hole through the middle of the puck and thread the bolt through. I have seen entire F250s sitting on body lifts made of 8+ pucks. If a stack of pucks can hold an F250 crew cab, it can hold a Kayak. Pretty cost effective too.
If you plan on holding over 200 lbs, then you may want to go to a roof track. But $1500 is kinda crazy for this and it will actually be more if you consider most people won't want it for trade ins. I wouldn't. But I don't think a couple of Kayaks would weigh more than 200 lbs.
Sorry, but a roof rack isn't rocket science.
And when has a roof rack warranty every been needed? The only thing that can break is the clamps or straps that hold the equipment to the rack. What a joke. If a strap breaks, It would be a Yakima/thule part, not the hardware. Just bring in the strap and get a new one. I think more likely is these guys are used to having people do what they say and want a sale. Nothing more.
If you plan on holding over 200 lbs, then you may want to go to a roof track. But $1500 is kinda crazy for this and it will actually be more if you consider most people won't want it for trade ins. I wouldn't. But I don't think a couple of Kayaks would weigh more than 200 lbs.
Sorry, but a roof rack isn't rocket science.