I've never actually put hands on the defender, so I don't know how much chunkier it is than the commuter. It looks like the defender layers are reversed; the hard candy shell inside, and the rubber around that? Try putting the case in the dock without the insert, and without the rubber wrapper, and see if the usb plug reaches the phone. If so, it may be worth trying cutting the port plugs off. Otherwise, it depends how hands on you want to get with removing more from the dock than just the insert. But the standard docks are $15 on amazon, so if you hack it all up to pieces and it doesn't work, you've not lost too much in the name of science.
As it happens, I took my dremmel to my car dock last night and it was promising at first, but by the time I got enough material removed for the phone to sit in the dock with the case on, it was being held less snugly than it is in my standard dock, and I hadn't even worked out how to get the usb plug to line up right. [sour grapes] I hate the car dock launcher interface anyways, so I'm just going to buy a second standard dock and mount it to my dashboard.