Heres my opinion/speculation of how it'll work.
The system is the handheld. The dock is just a dock, no special thing to make it more powerful because that'd just be pointlessly adding to the cost and Nintendo doesn't really care from what I've seen. Which is fine with me. The cheaper it is, the more games I can buy at launch! Bring on that X1!
People aren't trying to say that the dock will have special hardware to make it faster (well outside of one or two maybe). The handheld running faster in the dock would purely be down to the fact is could provide the system with more wattage and help cool it. Therefore while it might be limited to say 500mhz in mobile mode (which x1 would be due to its power usage) it could then run at full 1Ghz in the dock.