The Apple dock cannot take the bumper, you need to take off the bumper.
I need a dock for work and at work where I can just slip my phone in (bumper and all).
Amazon sells a dock from Oriongadget which will allow you to dock an iPhone with his bumper. It will cost you $23.00.
Probably, not due to the large variation possible with iPhone cases it would be difficult for a exact fit to a specific dock you would almost nead a special dock for each case out there.
The good news is that there is a very good compromise solution and that is a dock connector extension that will allow the iPhone and case to be raised out of the dock and clear most obstructions with most cases and iPhone / iPod docks. Something such as the Dock Extender by SendStation should do what you want.