The other day, my wife and I were picking up a swing set for our two boys. The swing set came in four boxes. Two of the boxes stuck out the back of the 4Runner by about two
I don't have an answer to your question...it would be nice if there was a tie down provided. Otherwise, you just have to anticipate this and bring straps for the roof rack. Or, lower the rear window and smell the sulfur!
I hauled a few 2x3's without my trailer. So what I did was lay-down the backseat, position it best I could, then using the latches on the back I bungeed/anchored the wood in place so it would not slide all over. It worked out really well.
The roof rack has a weight limit and will affect the handling if it is heavy (even more top heavy). Plus you have to load it and unload it from there (scratch & dent risk). I'd put my bike or kayak up there but I wouldn't load to much lumber or an outdoor playset up there.