I actually prefer the look of the van without the body mouldings so I won't be putting them on. I think when they are placed higher, they interfere with the flow of the "bolt" as the angles are different, so if I was to add them, it would be where Honda specifies.
Until my cars are several years old, I tend to park a bit away from the crowd and never try to fit into a tight spot, just to be closer to the mall entrance (walking is good exercise for me). I also try to park in an end spot with a car only on one side (cuts the chance of a door ding by 50%).
Sounds like I'm a bit odd, I guess, but our 2008 Sienna had no side damage Nor did my car before that. I don't rely on the mouldings for protection because there is always some car design that misses the moulding when their door is opened. A good example of this are cars that have rear doors that form part of the circle of the rear wheel well. No moulding can protect you from those nasty, pointy edged doors hence my self imposed parking rules.