You need to post in the Freeflow Core forum to get a proper answer as it is a specialized product.
I process a lot of word documents which have a mixture of orientations.
As a long time user of process manager I would use the route feature to select ALL PAGE ORIENTATION SAME: No and export to pitstop server to change all page orientation to the predoment orientation of the document then reintroduce the amended file to the workflow.
Is there a similar feature in Core?