I carry Kayaks on my Rogue using the factory roof rack and cross-bars and have never had a problem.
The spacing is a little closer but I think that is due to the roof slope and the fact that it's a "compact" crossover and not a full-blown SUV with a massive roof.
Once everything is mounted and tied down, it is just fine.
I use Thule 835Pro folding-J kayak racks
http://www.thule.com/en/US/Products/Wat ... 31306.aspx
I carry 2 kayaks, an Eddyline Merlin LT 13.5" composite (14.2") and a Current Designs Kestrel 120HV rotomolded (~50lb).
Make sure to use the tie-down straps in the front AND rear.
When tying down in the front, I screw in the tow hook.
When tying down in the rear, I hook it to my factory tow hitch.
If you don't have a tow hitch, there is a standard hook on the right side"tucked away" underneath but that will cause the tie-down strap to run at an odd angle, also it will catch on a metal edge and over time, will probably cut through your tie-down line.