I’ve been using docker directly for a while and haven’t encountered any issues. I also haven’t found any TrueNAS specific quirks.
On the command line, docker and docker compose works. I’ve also been running portainer for some time which also works. Other users have reported using dockge instead.
Note that docker containers will not show in the TrueNAS Web-UI. But that might be a feature that is added in future versions.
Of course there’s always a possibility that a future update will break things, but that is can always be the case with any system.