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Not saying there aren't any benefits to docker, migration to a different host distro and dependency conflicts are the big two. But for me they are kinda the only two, I find for what I do it's just as easy to write a shell script that downloads and unpacks software, and copies my own config files into place than it is to deal with basically doing the same thing, but with docker. I could use ansible or something similar for that, but for me, shell scripts are easier to manage.
Don't get me wrong, docker has its place. I just find that it gets in my way with it's own quirks almost as much as it helps in other areas, especially for web apps like Nextcloud that are already just a single folder under the web root and a database.
One additional benefit I get from not using docker, is that I can do more with a lower-powered server, since I'm not running multiple instances of PHP and nginx across multiple containers.