For the server setup I would use a dedicated sata or SAS card. They are more reliable and add flexibility.
For operating systems I would go with Truenas on bare metal or Proxmox with PCI passthough to the PCI sata card to a truenas VM. ZFS and therefore truenas benefit from lots of ram and a multi core CPU. With your 3 hard drives I would get a 6 core CPU and at least 32gb of ram. More ram would be better.
I have no idea what your budget is but this setup isn’t cheap