A more traditional box-making method would give you a stronger result. The problem with simply cutting a deep pocket out of a board is that while the side walls that run parallel to the long grain of the wood will be strong, the ends that run across it will not; they're just end-grain and subject to chipping away. If you want to do that anyway, I'd suggest doubling the thickness of the end-grain walls.
It is important to hold the material absolutely still when machining it. Warpage is often going to be a factor when dealing with wood, but some species are worse than others in this regard, and wetter wood will warp more than dryer wood.