I watched the video. Yes, if your sandbox config is weak then it will allow sandbox escapes. I agree the should default should be a secure sandbox. Bubblewrap offers the opportunity to shoot yourself in the foot. Look into the others tools I mentioned if you want to see different implementations. Sydbox is the one I think is the most interesting.
You can layer packages using
rpm-ostree install $pkgname
. It uses fedora repos. You can also (preferably) use a distrobox or toolbox container with a non-atomic distro and then install the desired package. Generally better to avoid layering packages but it works fine in my experience.