The 2000+ Bonneville uses a "docking" type of system instead of a harness and plug. You push the factory head unit into the opening and it docks into the antenna connection and power/speaker connection at the back of the cavity. That means there's very limited depth in the opening unless you actually dismount the connectors and push them back out of the way. It's a PITA car to install a head unit into, actually. Usually you can manage a flush mount with the right kit, but if you have a deeper-than-normal head unit or lots of RCAs or connectors at the back, you might have problems.
For the original poster, you might have to dismount both the power/speaker connector and the antenna connector, and possibly cut some plastic afterwards to make your head unit fit.