When I shaped those panels on the patterns and in the CNC kit I allowed some extra material at the bottom so that the bottom edge can be accurately trimmed to fit flush with the inner face of the plywood bottom. It is better to have a bit of extra to trim off than to find that it is a few mm short. I only do this on edges where it is practical to add a bit extra, not all edges. Other examples are the hull skin panels, which are a bit longer than needed, then get trimmed back to the line of the transom and the cabin roof, which can be trimmed in both length and width.
DD