If we are talking Silverblue then podman is your pick for everything Flatpack “can’t”
there is no big push for cli flatpack since this already a solved cause with containers for podman/docker/kubernetes
however no matter how you approach this you will always have dependency security issues
unless you built every flatpack/container yourself you are at the whim of the creator of it to keep every dependecy updated
this is already a known vulnerability factor in the container sphere on topbl of the threat of 0-day exploits
hope this helps with the dumbster fire of the virtualbox version in the official Ubuntu repositories
(virtual box basically “breaks” on Ubuntu LTS once a newer HWE kernel gets released unless you install a newer version of it, leading to hundreds of support threads every time this happens)