A deeper look tells us it's not that simple (as deeper looks often do). A lot of those statistics include Pagano's time as Chargers quality control coach, assistant linebackers coach, outside linebackers coach, and linebackers coach. Pagano has only been DC since 2012.
Manning's passer rating against the Chargers in Pagano's time as DC (note: since it's 2012, it's also all with Manning with the Broncos): 107.2. That's better than his career average with other teams.
Stew on that, NFL Network.