EDIT: Wow! thanks for all the detailed and super quick replies! I've been reading all the comments here and am concluding that (even though I am currently running only one service) it might be interesting to start using Docker to run all (future) services seperately on the server!

This is pretty much what I've started doing. Containers have the wonderful benefit that if you don't like it, you just delete it. If you install on bare metal (at least in Linux) you can end up with a lot of extra packages getting installed and configured that could affect your system in the future. With containers, all those specific extras are bundled together and removed at the same time without having any effect on your base system, so you're always at your clean OS install.

I will also add an irritation with docker containers as well, if you create something in a container that isn't kept in a shared volume, it gets destroyed when starting the container again. The container you use keeps the maintainers setup, for instance I do occasional encoding of videos in a handbrake container, I can't save any profiles I make within that container because it will get wiped next time I restart the container since it's part of the container, not on any shared volume.