There is no way that Andrew Bynum can effectively defend Chris Bosh. Bosh is far too quick for him and has a lethal + hugely efficient face up game. Terrific first step and is a foul drawing machine in matchups like this.
Bosh will pull Bynum out of the paint and put in difficult defensive situations all game long. Both from a man-to-man standpoint and in providing effective rim protection (which likely opens up their entire defense). Bosh can collapse their defense.
Sure, Bosh will have some problems with Bynum's size and power game in the post ... but, simply put, a Chris Bosh led team (with Bosh defending Bynum + a quality team defense) will be able to defend Bynum better than Bynum (and his team defense) can defend Bosh.
Plus, Bosh can play 20-25% more minutes than Duncan can.