If you can’t configure the utility to ignore the .DS_Store files, it would likely be better time spent building an Automator service that you can run on the folder to delete the file before processing the folder.
I’m not with my Mac at the moment, so I can’t offer a workflow to use. I imagine, based on the inability to see the file using cmd-shift-., it will need to use rm command in bash, possibly with find.
With the Automator solution, you’d just have to right-click on the folder and choose the service from the Services menu.
On another tack, does the PDF utility offer any support for some pre-process functions. If so, the same routine used in the Automator Service could be used to clean the folder before the utility processes the files.
Additionally, it may be possible to call the utility from the command line, you might be able to run a script that cleans the folder, then runs the utility to process the files.
What is the name of the PDF Utility? If I can get my hands on it, I might be able to come up with a solution.