I don't think the W3 fits in the box. The difference between the vantage and the original JL is that vantage is thick plastic, and the JL audio is fiberglass. Really, I don't think anyone will notice the difference. I have the vantage and was amazed at how heavy it was. At least a good quarter inch of thick, heavy plastic all the way around, sides ribbed for extra strength on the sides to avoid flexing.
It is also possible, I believe to get an empty MTX as well, which is also made of plastic. Give them an e-mail or call, their customer service is pretty awesome.
In the cases of all the boxes, it's really tight fit behind the panel, and regardless of the make, if it shakes it shakes because the boxes are so small, the reason why all of them come with mounting equipment to fasten them to the car itself. So either way, it'll pretty much be the same. The sub itself will probably make the most difference.