Yes, the space below is just left empty for water. The bottom tray right above that could hold Eheim "Mech" (a ceramic ring mechanical media that is nice because the inside diameter is larger than many other types of ring media) capped by a coarse sponge (you'd have to cut that from a sheet of coarse.) The next tray up could hold a biomedia like Seachem Matrix capped by a medium sponge (some LFS will have big sheets of sponge or often you can find some other brand that makes the right stuff in a size that can be cut down.) The top tray could hold more Matrix (or some smaller grained biomedia) capped by polyfloss.
This is just an example of how you can customize. You can also find out what the original intent was for these trays and you might even be able to get pre-fit sponges intended for the which might be helpful.
~~waterdrop~~