If it was me, I would put the mat in, set the storage box on top of it to mark it, then remove it and cut it into 2 pieces. One with stay in the storage box the other would just be a floormat. Late fall through spring can get fairly messy and muddy here and I want the ability to remove them so they can be power washed. If you don't have sticky mud to deal with then just brushing them off would work fine.
If you prefer a 1-piece mat (covers the center hump) than I would go that route. It appears to be more of a rubber mat which may be good or bad?? I don't know if anyone has these yet so you might be the first to try them. I and a few others have the 2 (or 4) piece mat sets. They are molded to fit the interior and are similar to a Weather Tech floor mat. They work great with the Razor Back Offroad center console where the 1 piece would not work at all. They look and fit well and don't move around. So, it's really up to you whether you want a mat that covers the hump or not.