Actually, using your stats, Bogaerts was slightly less likely to "swing" at the first pitch (Bogies was at 4.6%, Pedroia 4.75%). I put swing in quotes because those stats only reflect how often an outcome results from the first pitch (how often the ball is put into play, excluding HBP). They do not reflect if a batter swung and missed on the first pitch or fouled it off. Anecdotally, those probably didn't alter the numbers very much. No hard data to back that up, and I'm not going in and review every play-by-play to find out.
The overall point remains, they are not doing themselves any big favors by taking virtually every first pitch. I don't think anyone is calling for a major overhaul, just a tweak in the thought process. If you get a particular pitch in a particular spot on the first one, hammer it. Otherwise, let it go. Make the pitcher adjust and try for that perfect strike (the kind you don;t want to swing at unless you have 2 strikes). That and learn to foul off tough 2 strike pitches.