I agree some software doesn't fit into Docker-style application containers well, but I'm still a fan of Infrastructure-as-Code. I use Ansible on LXD containers and I'm mostly content. For example, my Flarum forum role installs PHP, Apache and changes system configs, but creating the MySQL database and going through the interactive setup process is documented as a manual task.

I could automate this too, but it's not worth the effort and complexity, and just documenting the first part is about as much effort as actually scripting it. I think it's a reasonable compromise.