I have been building large assemblies (1000 to 3000 parts) and have been using skeleton parts to control assembly positions and space claim. I have read a few articles that recommend only using surfaces, sketches and planes. Is there a specific reason not to use solid bodies in your skeleton parts?
I use solids in base/skeleton parts all the time, top down design is the only way to go IMO, and it's never caused me any issue that I was aware of, as long as any extra bodies get deleted at the end.
Maybe so they don't inadvertently skew mass property queries?