I assume that the synergy stats account for the value of the player being defended. It's as much about how many points they score as about how many fewer points they score. Otherwise the best defenders would be all among bench players.
Subjectively, I always felt that part of bargnani's help defense struggles was that he's very reluctant to leave his man. Much too often I've seen him glued to his man while another player goes uncontested to the basket. Would be interesting to analyze why that happens, I suspect part of the reason is he doesn't know how to properly make that decisio. To leave or stay, part because he's lazy and part because he's been accused too often of being a poor defender that he's afraid to leave his man score.
But the truly relevant point is that even if you call him elite (which is pretty crazy), his help defense is so poor that it more than negates his strengths. Otherwise, how can one explain his horrendous +/- stats, especially given his good offensive skills. However, last season there were some promising signs early, and we can only hope that his poor performance in the second half was due to his injuries. We'll soon know, and it would be fantastic for us if he can finally turn that corner once and for all.