i.e. you want a Constructive Solid Geometry tree that includes regularized set difference operators 
GC3 ship design is currently an additive-only solid(?) modeler (N.B. not a surface modeler), i.e. a CSG tree with only union nodes. Since Boolean union is associative, order is irrelevant, and the "tree" collapses to a flat list (actually, an unordered sequence).
Machinists have had the inverse problem forever, i.e. they make protrusions by applying material-removal operations to the space around it. Hence the gee-whiz nature of today's 3D printers.