My setup is pretty much option 1, I have no issues with it. You can easly mount NFS shares as docker volumes (I m docking that for jellyfin and nextclould) but you need to get the permissons right. But I am no expert, just a hobbiest not smart enough for a better solution :)
Try Zotero. It is a complete literature databas but it’s PDF reader is very good at extracting images and text. Works on all OS, web and mobile. Native Linux client has been very smooth for me. Oh, terminal it doesn’t do though. If you want to extract a large amount in an automated way, its probably not the right tool.