Flatpak standing the test of time: modern Flatpak apps running on Ubuntu 16.04 ESM, a 7-year-old distro
According to Door Knocker, almost half of the portals are unavailable on Ubuntu 16.04, compared to only one unavailable on Fedora 39 with GNOME, which means Flatpaks running here may have more limited capabilities than usual.
They are talking about the code sitting inside the flatpak I think. If a developer fails to continue updating the system libraries a flatpak contains, you retain old vulnerabilities you could have otherwise fixed with a sudo apt update && apt upgrade or a sudo pacman -Syu
Flatpak has relatively weak sandboxing, takes up a lot more storage because sometimes dependencies get bundled a few dozen times, and most distressingly depends on the application developer to be available to do things like address supply chain attacks.
I don't think you understand flatpaks. Flatpaks have dependencies such as the gnome or KDE frameworks. Those frameworks are only installed once so I'm not sure where you are getting the idea that they are installed multiple times.
Also flatpaks usually come from flathub.org which is unlikely to be compromised. It not impossible but they seem to be pretty good about properly labeling apps.