The majority of lifters do bring the bar down to the upper chest level when inclining. I noticed that some lifters who lift their butt off the bench while inclining turn the incline into an almost prone bench. Those guys bring the bar in lower on the chest.
Regarding Branch Warren method I think you shouldn't even consider what this enhanced professional bodybuilder is doing. Bring the bar down to where it feels the most natural to your structure. For most it's the upper chest. It should feel pain free to your joints.