Its kinda hard to get really custom with the limitations of MDF. Even with imagination and creativity, youre going to have flat surfaces, corners, and edges which will increase in complexity with more angles if you choose to persue a custom MDF fabrication.

Some ideas for that space might be building enclosures on each side of the hatch area which comes out flush with the strut towers. Check for air space requirements. This arrangement in MDF is going to create alot of difficult angles and sealing issues with the box in that space.

If you dont want to retain your spare tire, you can build a box into the wheel well and have them firing up. To add a custom touch you can order a fiberglass tub or plate to mount your subs to and have it painted to match your vehicle, although I think this theme was so overplayed in the 80s-90s it just doesnt look modern anymore.