I use the LR supplied cross bars and they work just fine. I have thrown up kayaks, canoes, surf boards...you name it, regularly for 10 years. Only issue is the rubber insert in the top of the bar can creep out when you slide heavy loads on it. Pops right back in, though.
I don't have a custom kayak rack. I just throw the boats on upside down. I have put on 3 kayaks at one time (one on the side, tie it...then lean the second, tie it...then pile on the 3rd), but it's usually just 3.
Canoes are a little trickier for me due to the placement of the cross bars. It is really hard to get a canoe on upside-down without the bow or stern scrapping the roof. As I don't have to do this often, I just put it on right-side up. (I also have a hitch extender bar that sticks straight up from the back to hold the ass end.)