I can’t say how much work it will be to get nextcloud running in a VM. You have more control, certainly, but you also need to do more manually to get things running. It’s also less resource efficient since you need to preallocate CPU, RAM and storage.
If there’s any comfort, it’s that docker will become the apps subsystem in the next version of TrueNAS, 24.10. Planned release next month. Maybe that will be easier for you to maintain?
Read more about the next update here:
