Oh wow! Quite a journey!
I’d consider Paperless a hall-of-famer for self-hosted software and something most people who get into self-hosting discover at some point, even if they don’t use it.
So thanks for building it, even if you’ve moved on. You gave the forkers something great to build from.
My solution to this has been to not forward the ports on individual services at all. I put a reverse proxy in front of them, refer to them by container name in the reverse proxy settings, and make sure they’re on the same docker network.