I did not consider the thickness of the boards because I was designing for these "modern" cabinets that have no significant gaps between the parts when viewed from the outside. So board thickness is just an implementation detail :)

But yes, the real designers using the CAD needed to take board thickness into account when designing the internal structure. In other words, this tool is generating a list of my requirements (what I want it to look from the outside + the labels describing what I want each part to be), and then there's the separate work of designing the actual, reality-constrained furniture.