Okay for those curious, yes indeed it was a permission issue. I think due to me using the WEBUI on the Synology to transfer the data from the QNAP -> Synology, "users" group somehow didn't get added to the Media folder. Once I explicitly gave the "users" group read only acces, the Plex app was able to access the data.
TL;DR -> Make sure the permissions are set correctly and have both users AND groups added.