Yes, copying the entire config directory will create a backup. I run homeassistant container and use a cronjob to do the backup. I posted about it here.
I’ve noticed for a proper backup its important the container is stopped and the backup command happens under root to get all files.
I then use the built in backup utility in Ubuntu to copy the backed up directory created by the rsync command to Google drive.
It doesnt make much sense to run a docker containerized environment in a VM. You shoud install docker right on the host Linux os if you go this route and not in proxmox. You will have endless problems passing usb sticks through the vm and containers if you do this.
Docker on Proxmox | It's full of stars!.
The is no comprehensive guide to do all this. You have to find the equivalent docker image of each addon you used and install and manage them all yourself. It is a lot of work but does give you much more control over everything.