I have the same issue and this is the response I had from CommVault Support:
"With filters set, it will filter from both backup and archive. There is not a setting to only filter files being archived.
The best way to configure it the way you would like to would involved two backup sets.
One can be configured to run Archive Jobs with the option under content "Only backup files that qualify for archiving", so that only stub files get backed up once the files are archived and you can configure the filters here.
The other one should be configured to just run regular backups, it will also backup the stub files that the archive backup set has stubbed."
Looks like there needs to be a separate subclient for archiving, despite what you would expect from Onepass.