Actually, every building has its own defense stat. Remember when I first started and I was posting the Limited Time Building and posted one with the upgrades along the Defense stat? Everyone was asking "Is this a defense building?" even though it wasn't. Yea, it's that stat.
http://forums.gree.net/showthread.ph...ocorp-Research
This is the thread. People were asking about the defense. This is the defense referred to in Raiding. When you raid a building it goes against the Building's defense. When you attack a player in PvP or other such events such as World Domination, that is when you are facing the Player's stat.
With that being said, we can understand the confusion as per the statement in your middle paragraph. We'll discuss ways to make this more clear.
Does this help clarify some of this confusion?