Pop bumpers evolved from the static bumpers of early pins (incl. flipperless games) that scored points and/or lit objectives. They are great for adding ball action/velocity/randomness.
I think what you're questioning is the relatively recent trend (by Stern) of almost always placing the pops (generally 3) in an enclosed area (the "pop corral") with one or 2 entrances and exits. (I know this was done in earlier games too, but now it seems to be their only pop config.) I'm not a fan of this because it is a pretty lame configuration. Ball bounces around the enclosed area (oooh, loud and fast thunks!), scoring little and having negligible effect on the game, annd then dribbles out a corral exit. Pop bumpers are much more fun when they are exposed to the main playfield and flippers. Compare the pop bumper config of pretty much any recent Stern game to games like CV, TZ and many other Pat Lawlor games, WOZ, almost any EM game and many many SS games. When the pops are exposed on the pf, it really adds to the action. When they are confined to a corral, not so much.