Well, they differ quite a lot when it comes to surviving flamers. In fact bunkers as a separate modifier is something i enjoy.I had always assumed that emplacements were considered bunkers (because of their size?).
Towers versus hardpoints should be balanced by firing through, i think: hardpoints should be harder, but don't shoot through each other, while towers are taller and shoot through anything. (but right now i heard that we have just opposite)