Sync does work for me. I only noticed, once I restart the server, the Kodi clients are no longer connected and need to be restarted too.

Use LXC unless that's for some reason not possible. It has less overhead than VMs. How many services you put into one container is for you to decide. I have one for jellyfin and one for the arrs and download client. Splitting everything into more containers might be beneficial, if something stops working. You can then fix or use a backup for the one thing without inhibiting the other services.

Unless you want to use docker. Then, as others have mentioned, make one VM and put all your dockers there.

Probier mal mboxviewer. Ich weiß nicht ob der in der für dich richtigen Ordnersruktur exportiert, aber ist auf jeden Fall ein klasse Tool das mir schon öfter mit mbox Dateien weiter geholfen hat.

Did you even bother reading the first paragraph? There are other reasons for wanting subs besides not knowing the language.