Shout out to Michael Davis. He read about my BRL-CAD STL problems and suggested I use combinations instead of regions. This largely fixed my STL export issues, and the export is generally much faster. I still have to check that a service bureau can use the STL files produced. Here is a render of the STL output:
You can see the faceting produced by the chosen resolution. Looks like we are back in business with designing and producing Polywell cores.