You could try making 2 pdfs one with filter on and one with filter off, however the pdf user cant turn the filters on off
But further to this if you use the bentley pdf.pltcfg and allow it to make a layered pdf so the people using the end pdf can manipulate the on/ off levels and ref files on and off would be helpful to the end pdf user
especially if you provided some training or instructions on what your providing and how to use it..