Hang on a minute - you say “PDF Folders”. Are you not putting the PDF files into the same folder as the tracks, i.e. into the Album folder, but instead into a sub-folder that is in the Album folder?
If that’s the case, then no wonder you don’t see the PDFs in Roon - Roon expects to see artwork and PDFs in the Album folder alongside the tracks. It currently doesn’t look in Album sub-folders, as @Pieter_Vroon points out, and has been noted here: