As per NBA.com, the TEAM defense improves when Bonner plays. The entire TEAM (re: Spurs) give up fewer points per possession when Bonner is playing. Must be that help defense Duncan offers.
Numbers for 2012-13 are probably still not statistically significant, but when you look at entire seasons over the last four years, that's something. And it's a nice trend. Duncan's help cannot be the entire reason for Bonner's improvement as Duncan gets older.
Shoot, some mortarboard guy on this site says that Duncan can't move laterally anymore. Apparently that only applies if he's NOT helping Bonner.