I host synapse as docker container behind traefik and it works pretty well. I have two users on my instance, have setup the mautrix-whatsapp bridge and federate with the instance of a friend.
The setup was straight forward: Pointing the sub-domain via traefik to the service and in the homeserver.yml enable well-known which announce port https with port 443 instead of 8448.
As recommended from others here the docker version with a compose file works great.
I had similar problems with nextcloud upgrades until I switched the channel from latest to stable. Stable is still version 31, but I haven’t found a user comfortable alternative which I can give my family without hearing their pain. For me *Dav is the best decision and Syncthing for files that should be offline available like keepass or something.
And if you are actually on latest/32 maybe it is an option to switch to a tagged 32 version until it becomes stable.
From my view a major update shouldn’t been done automatically.