is there a protective case, not skin, that would cover and protect the device without the need to remove it to place it in the car "cradle" or media dock?
As far as I know, the answer is no. Seems strange, but that's the way it is. Sometimes, I get the feeling that new smartphones are coming out on the market so fast and furious that accessory manufacturers can't keep up, or if they try, sometimes the products are a lesser quality than earlier ones.
Best solution here is to abandon the Droid X dock. Get an aftermarket holder (arkon makes a good one). Then you can use it with any case and any phone that you have.