Yup, it does - it actually fits in there by default. In order to get it to fit snuggly without the extended battery, you have to put the extra plastic sleeve on the car dock.
It also fits in the Standard dock and HD dock with the extended battery
I have a navigation dock and an HDMI dock. Just got my extended battery today and the Droid x2 with extended battery DOES NOT FIT in either.
What type of battery life are you seeing with the extended battery?