Improve server update process to prevent breaking due to stale configs that were not customized by users

[marcospgp]

#7193 (comment)

I run system updates to all of my servers periodically. Applying them to the cloud server Coolify was running on broke my Coolify instance due to the outdated Traefik.

But I didn't configure Traefik - and I'm happy to stay on the latest version. If there was an "auto-update proxy" setting, I would enable it. /2c