Ken- in my limited use oif this plugin I haven't seen a way to retain and control layers in the PDF. I'll investigate further - but the software trends towards presentation as opposed to manipuation. I've been stripping the last 8 models down to essentials, then doing a 'Save As' prior to PDF export.

I do know that you can show/hide geometry with a model outliner in the PDF. Not sure if this saves states as you resave the PDF.