As a person who has been managing Linux servers for about a decade now, trust me that a few hours or days of learning docker now will save you weeks if not months in the future. Docker makes managing servers and dealing with updates trivial and predictable. Setting everything up in docker compose makes it easy to recover if something fails, it’s it’s self documenting because you can quickly see exactly how your applications are configured and running.
Not necessarily. If you trust the code running on your device then there is no backdoor they could install on a server that would break e2ee. They would have to backdoor the client where the keys are.