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YunoHost "packages" are just scripts. In the case of Lemmy, Lemmy_ynh's install script actually fetches the Lemmy Docker image and extracts the files (including pre-built binaries) from it. And then it writes the config files to use the system Psql instance instead of a containerized version.
FWIW I don't care how YunoHost installs the apps. Whether it's fetching and running containers, or building from source, or grabbing binaries. As long as the apps work and the reverse proxy gets wrangled it's fine with me. Just in this case refusing to run the Docker images directly is, at least momentarily, a problem for updating the app.
I just telling why Yunohost will not switch to Docker. Running normal Docker app wouldn't be coherent with yunohost package managment. And how you can see, no containerization brings problem with updating some apps, not only with Lemmy, but - if I remember right - with Wallabag. Yunohost way of things has advantages and disadvantages. I use Yunohost for more than a year and I am not planning switch to Docker.