Here is the outcome:
Once you open the box, there is room for a 60 card deck (with a few extra cards). Unfortunately, the price label of the MDF was on the reverse side when I cut this, you can see it in the living hinge. It's not too bad, since this is just a prototype, and I will eventually cut it with nicer wood.
You can remove the left hand side to easily slide the cards out of the box.
There is also a small hidden compartment at the bottom of the box.
If you open up that compartment, there is room for a 15-25 card "side deck". MTG players can substitute cards from the side-deck into their main deck between rounds.