I guess the part I don't understand is - if you know that the Deform tool is making a messed up object for those spheres, why is it that you're trying to export that messed up object and expecting for the exporter to produce a good result from it?

There's a saying: "Garbage in, Garbage out" - if the exporter is given some kind of mangled object to export, it doesn't understand how to unmangle it, the solution has to come in the process that generated the messed up object to begin with.

Given a messed up object different programs will behave in all sorts of different manners - some may try to repair it (like SpaceClaim seemed to), others may give up or in the process of giving up may instead try to just salvage what they can make sense of which could result in a bunch of separate surfaces.

In the future I would like to add some tools to analyze objects for different ways that they might be mangled. I'm not sure when that will happen, it's a lot of work to plan a good UI for that. In the shorter term I do expect to work on fixing up the deform tools so that they won't construct a mangled object for deforming spheres.

- Michael