I don’t think YunoHost uses containers, at least it didn’t the last time I used it. It installs applications natively.

The best part about using containers for self hosting is that you don’t have to locally install dependencies for anything you want to run; they’re all inside the container. So if something doesn’t work, blow away the container and any data it created. Uninstalling a locally installed app can be a pain as you’re left with all the installed dependencies and any configuration that may not have been removed.

Another benefit of containers is that it’s generally easy to update an app to a new version by downloading and running a newer version of the container and maybe running a migration command. Updating a locally installed app means installing newer versions of dependencies before running any migrations.

The upshot is that I personally find containers easier and cleaner to deal with than locally installed apps.