Use gdalinfo to check you actually have a coordinate system specified in your PDFs. If no, make sure you have checked to Export Map Georeference Information when you export the maps from ArcMap.
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Adobe released an update to Illustrator 2021 (v25.3) that includes native support for M1 Devices and Rotate Artboard functionality. Please note these features are not yet supported within MAPublisher at this time. See compatibility notes.