I have run into this issue a few of times and recently I have been asked to put in a feature request. Currently there does not seem to be a way to flatten a PDF through automated means other than generating Laserfiche pages which tends to lose some annotations from the original PDF. We could use Snapshot in a manual process that should be able to accomplish what we want but from a Workflow and/or Import Agent standpoint were left with little to no options. 

Thanks.