Playing tough D on Bowen simply is not a part of many teams' game plans. They're more inclined to simply leave him open and put more pressure on Duncan/Parker/Manu.
That's why Bowen has developed his penetration game more in the past two years, because it forces someone to actually guard him. I've seen a lot of complaints about this facet of Bowen's game, but he's averaging a career high in assists (1.9) and his turnovers are the lowest they've ever been since he started playing heavy minutes.
People should take note of this when they see his shooting is down, because he's actually doing more to stimulate offense than standing in the corner and hitting or missing.