Sean,
Looking at the pic of the 18th at Red Tail, my guess is that the pond fronting bunker is a save bunker for a top shot. He left the water in play for a good player, but figured there is no reason to slow down play and frustrate someone who has already missed the green badly.
It also appears that the front edge of the lake isn't totally visible, so Brian may have thought it "fairer" to stop someone if they were trying to lay up, but couldn't tell where the front of the pond is. I'm pretty sure the bunker is blind, too.
As far as the two step penalty, many golfers would argue that a two stroke penalty for missing a long iron shot by inches to a few feet is too severe. If I find that I have "too many" greenside ponds in a design, whether natural or if they are man made for drainage, irrigation storage, fill generation, etc., I might take the two longest approach shots and bunker the edge for variety, and to give a little miss room on the longer shot.