If you use HAOS, then it’s a matter of installing the Matter (sorry) and Thread addons and you should be good to go. The official documentation explains this well.
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I am still flexible regarding the OS, but I thought about installing a "regular" Linux OS to give me a known environment for the home server side of things and install HA on top.
If you’re starting HAOS is the way to go. It’s really effortless and I'm considering to switch back to it from Kubernetes
I recommend this too. I'm using kubernetes for other stuff, but HAOS for Home Assistant. Super easy to manage. And it works great on small, appliance machines (I'm using Home Assistant Green).
That's the route I took. I still pray for a nice Home Assistant helm chart because I'd really like to be able to quickly bounce a Home Assistant container around between nodes and also have easier monitoring and alerting, but all the k8s options just seemed too jank.
Yes, but then I had to setup Multus to have Home Assistant have an interface on my LAN (i.e. for HomeKit) and it’s added complexity at that point
If I would use HAOS as my real OS (so not as an image for a container), that would limit my capabilities of running other services, wouldn't it? Sounds better to have HA containerized. I found this tutorial: https://sascha-brockel.de/en/set-up-thread-matter-in-home-assistant-with-docker/
Just use Proxmox to install HAOS as a VM
If you plan to run other stuff, I’d rather recommend using HAOS in a VM, possibly on Proxmox VE.
If you decide to install HA as container on any other host, then you will have to install any other component/plugin/etc as external containers or services as needed. HAOS has everything included.
Especially true if you want to play around with Matter and Thread
It's pretty simple: Spin up a VM or container with HAOS; do the initial Home Assistant config; and ensure that the ZBT-2 is assigned to it via USB passthrough. HA will detect the ZBT-2, and offer to add it to your instance with a card in the Devices & services settings. (I think it's more obvious these days, but they've made some changes recently, and I haven't added anything since then to see.)
Once it's added, you can then pair Matter devices with HA. That's most easily done with the Home Assistant app on a phone or tablet, but can be done through the web interface using the Add device button on the Matter page in settings.