I've not played CPC or Pasatiempo, or any other MacKenzie course to my knowledge, so I cannot comment about these specific examples but I disagree with the premise.
What is the purpose of fairway bunkers?
-suggest a line of play off the tee-
-create an obstacle for the player to avoid-
-penalize a misplayed shot at that distance-
All of these (and probably many others) help to shape the strategy a player will employ as he approaches the hole. A tree does the same things, but in a much different way. The tree is an aerial obstacle whereas the bunker is a ground obstacle, and thus needs to be placed in a different position, along the hole, than the bunker.
If MacKenzie placed bunkers under or behind trees I would bet the bunker better represented the purpose of the obstacle he intended, and was hoping to have the tree removed because it had lost its relevence.