Sorry when I said factory I meant factory on non-FJ vehicles. I'd just ask Vixx how they work on the utility rack.
Regarding other ways to attach your kayak racks, BajaRack sells "tent plates" that I've found pretty handy for mounting things. It's a small plate that clamps down over two of the crossbars. They're used to mount a roof top tent, but its simple enough to be adapted to anything you can bolt to it. You can get 4 of them for $60. Check out my photos of the bike rack I made with them:
Showing the bike rack from above. The 4 nuts between fork mounts are where I've got the tent plates bolted from below.
Showing the tent plate on the underside of the roof rack. I used 4 of these, but I think I could have gotten away with less. The tent plates are pretty beefy.