Can’t speak for OP but I can say that I switched to proxmox from just running docker and services native. Proxmox offers a lot of flexibility, you can do snapshots, build many different LXC containers very easily, to keep things separate or have better control over resource usage. Also I run mine in a 3 node cluster so I can do live migration of VMs and pretty quick migrations of LXC containers. This all allows me to run my services with little to no downtime and have redundancy.
With containers, most will have a persistent volume that is mapped to the host filesystem. This is where your config data is. When you update a container, just the image is updated(pihole binaries) but it leaves the config files there. Things like your block lists and custom dns settings, theme settings, all of that will remain.