4 days is a very short time and too soon for him to establish any habits yet. If you looked over the link I provided, you may have already read about some of this but I'll offer some thoughts here anyway.
Having the hidey box in the middle (like 1st photo) is actually a safer option. By contrast, having it against the side of the pen could provide too much of a launching point for him to hop over the side wall.
The puppy pad should be removed from the litter box. It has plastic and bunny may decide to ingest it, causing a gut blockage. The pads are not necessary. I'd suggest following the litter box setup described at the link provided (wood pellets [not shavings], topped with hay).
The connectors that come with the grid panels are not strong enough. Rabbits have been known to bump them right off. Better to use zip ties to hold the grids together. The added bonus of using zip ties is that it makes it super easy to create a "door" so bunny can freely go in and out of his cage during his exercise time. It is not advised to be picking bunny up and lifting him out of his cage for this. He needs to be able to go in and out himself. You can see examples of this on the same site in "housing options" under the "caring" tab.