you could have a fiberglass enclosure molded to the mdf but there really is no effective way to keep air from escaping unless you get a free air sub it is going to sound terrible. the mdf, while heavy, it is not heavy enough to keep the sub in place and limit flex enough to not let air escape...also the trunk floor is anything but flat. i recently covered my trunk in a few layers of peel and seal(cheap dynamat substitute) to eliminate exhaust drone.
you could build a shallow box onto the mdf trunk board you plan to make but you are going to run into some issues
1. shallow mount subs dont sound near as good as normal mount subs
2. shallow mount subs wont handle as much power, assuming you already have an amp
Boston Acoustics makes a sub:
Boston Acoustics SPG555-4 Oval 4-ohm component subwoofer at Crutchfield Signature
and a Tunable Radiator
Boston Acoustics SPG-TR Tunable Radiator [audiojunkies]
When you use these two together, not sure if thats the correct radiator or not but you can make a box that has half of the cubic ft. requirements of the sub and still get the same sound. im not sure how large your current sub enclosure is now, but im guessing its large enough that you need more space.
Also, short of a full custom fiberglass enclosure, there is no way to get the result you are after that will be as effective as the one i pointed out above. it may work, but once you turn your stereo up you will get terrible bass response if any and a huge rattling piece of mdf in your trunk. i have personally heard the SPG-555 in a radiated enclosure...it sounds amazing when tuned right, and it only takes up a fraction of the space of a normal enclosure