Fairly recently, Shapeways added its "MeshMedic" feature that unifies overlapping meshes when they are uploaded (or at least eliminates overlaps), in addition to trying to fix other problems with the mesh such as holes or flipped normals. However, even before that, Shapeways never said that overlapping meshes were a problem, so I'm not sure why they are for Printapart.
I did recently receive a full-color sandstone piece from Shapeways that was modelled with various overlapping components (each with its own UV map), including some text that I had embedded into the base. Some of the text had fallen out, leaving letter-shaped holes in the base. I suspect that in an effort to "unify" the meshes, MeshMedic did a boolean subtraction of the lettering from the base, leaving the lettering as an adjacent rather than an overlapping mesh, with color mapped onto the adjacent faces as well as the outer faces. I've been assuming that color mapped onto parts of meshes that are inside other meshes is simply ignored, but maybe I'm wrong in that assumption.
Last edited: Dec 30, 2010