If it's working - that's fine. Creating dependencies can make things more complex (you now need two systems running for one service to work) - but also isolating 'concerns' can be beneficial. Having a single "file server" lets me re-build other servers without worrying about losing important data for example. It separates system libraries and configuration from application data. And managing a file-server is pretty simple as the requirements are very basic (Ubuntu install with nfs-utils - and nothing else). It also lets me centralize backups as everything on the file server is backed-up automatically.

Things can be as simple or as complex as you want. I will re-iterate that keeping a "one server per service" mindset will pay off in the long-run. If you only have your desktop and a Pi then docker can help with keeping your services well isolated from each other (as well as from your desktop).