Using the plugin “Exclude areas from comparison” you can exclude defined areas from the comparison documents.
An area is defined by four number values: x, y, width, height - representing pixel coordinates. The values are relative to the pages as they would be displayed at 72 dpi. Multiple areas are supported as well as excluding an area from a specific page.
The plugin can be installed / activated in the plugin store of the i-net PDFC server / standalone application.