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Someone already said the firewall, and that’s the most straightforward answer, but there’s lots of stuff a server can be used for and most of those have some facility for making a distinction between unauthenticated users and authenticated ones. So as a second recommendation: use the permissions system.
What are you actually trying to do?
Have you considered using Quebes?
I might just be tired but I'm having a hard time understanding what you're asking.
We are all tired on this day.
Okay, what do you want?
"Quebes" maybe means QubesOS, so you are searching for an operating system, but since you mentioned problems with GPUs, you probably have Nvidia cards and to that I can only say good luck getting Nvidia cards to run with docker.
If I understand your question, you can just assign some of your server endpoints a public IP/URL and keep some others behind the firewall. My home lab exposes some services to the open internet, while others are only accessible with a VPN.