I see absolutely no reason not to use a two-door JK as an overlanding vehicle. Yes, you need to modify your kit to suit, but it's looking at things the wrong way to lament how much less space the two-door has than the four-door. Think instead how much more cavernous it is than a motorcycle. For a single person or a couple you should have no problems.
You could still easily fit in the back of that vehicle a tent with standing headroom, full-size cots, and a nice propane kitchen kit. Check the Summer 2009 Overland Journal for suggestions there, such as the Worthington aluminum propane cylinders, which are not only light, but narrow for storage as well.
A dual-height load platform is a godsend on vehicles such as this. It made a huge difference in my FJ40, and seems to very nearly double the practical load space.