NextCloud is a prime example. Adding some extensions (apps) on NextCloud becomes almost impossible when installed via Docker.
We have two teams with their own NextCloud installations. One is installed on bare metal, and other one is a Docker setup. The bare metal one is much easier to update, add apps, diagnose and operate in general. Docker installation needed three days of tinkering and headbanging to get what other team has enabled in 25 seconds flat.
To prevent such problems, JS Wiki runs a special container just for update duties for example.
I'd rather live document an installation and have an easier time in the long run, rather than bang my head during some routine update or config change, to be honest.
I document my home installations the same way, too. It creates a great knowledge base in the long run.
Not all applications fit into the scenario I told above, but Docker is not a panacea or a valid reason to not to document something, in my experience and perspective.