I think I have posted this before but I will again. I fished in the surf for a lot of years. In 1992 I bought Yakama ski racks. The double. They lock. They bolt to existing racks or have an adaptor that will make them fit anything.
Fast forward to 2008. Yep, still on my truck (4 trucks since I bought them) still work fine and no one has ever stolen a rod or reel off my roof. You cannot go wrong.
I have the Thule double ski rack - it's about 15 years old and it works fine! Bolting it on the roof is a must. The only loss I had was when the thief cut through the brackets. No way to stop that.
I have the Hunter 2 rod holder for my 4 Runner. I think its great. I haven't noticed scratching from it. I know people that have but some silicone around the edges to stop it. My Van Staals are beat to hell so I didn't bother doing that.