Using Automator CLI with passed file name
MacOS (OSX) used to have a Terminal command quartzfilter, which would apply a Quartz Filter to PDFs and allow output names. Sadly, it was removed in Snow Leopard. 

Here's a python script which works as a replacement.

The Automator action "Apply Quartz Filter to PDF Documents" applies the filter to the input, so your workflow copies the PDFs but then over-writes the originals with the Filter.