Make sure you have a plan for hard drive space. Mini computers tend to not have as many bays for hard drives. And since you're doing the media server thing, you'll want to be able to easily drop in more drives at a later time. You could do this with like an external USB hdd enclosure with multiple bays, but if you go with a desktop form factor that wouldn't necessarily be required.
Speaking of hard drives, checkout MergerFS, you can use this to pool multiple hard drives into a single mountpoint so you don't have to worry about moving files around to maximize disk usage. Also, the nice thing about mergerfs opposed to say RAID is all of the drives can be different manufacturers and sizes.
Also, I would personally recommend going with proxmox as your baremetal install and then spin up VM's for the various things you plan to run.
And if you think you might get more into the *arrs (like readarr or lidarr), it's probably worth your time to setup prowlarr.
And if you haven't yet, I recommend learning how to use Docker and docker-compose. There's a bit of a learning curve to start, but you'll save a lot of time and headaches in the long run. Linux-server has some good docs and images to get you started: https://docs.linuxserver.io/
And don't expose your *arrs to the internet, if you plan to share your Plex/jellyfin, then setup Overseer to support requests for new content.
Hopefully this all helps. Feel free to ask me any follow up questions as I have a similar setup (albeit with a bit more going on).