Both have the same exterior dimensions however when you open the lid what you see will be different. Inside the subwoofer console is a black tray for cds and only about the depth of a cd. In the non sub console there is a big white bucket that will fit a small backpack, netbook, or your lady's purse. Either one could be used for adding a subwoofer you may need to make changes to the sub model (cd tray) you WILL need to make changes to the non-sub model (bucket).
When I ditched my factory sub (which I had upgraded) I replaced the whole console b/c I wanted the non-sub unit for storage. Ordered from jparts.com and got a nice price.
Now that we're a few model years beyond TJs you should be able to find a console on ebay...make sure to get the one for your year as they evolved over the years (cupholder section).
Center console sub enclosure instruction thread: