That is not an "in-tank filter". It's the overflow box, and no, I would not recommend adding media there.
If you're talking about mechanical filtration (e.g. socks, filter floss, roller mat, etc), that will be best used in a high flow area of the sump so that the maximum amount of water passes through it. In most cases, mechanical filters are put in the area where the water enters the sump.
Regardless of whether or not you use this area for mechanical filtration, it's not a great place for a refugium.
The main biological media will be your rock; if you don't plan to have much rockwork, you can always put something like Marinepure or Matrix in the sump.