Even disregarding the trust issues with Flatpak packages made by random people: Packages often contain versions of some libraries in order to not depend on the distro's. If there are security vulnerabilities in a library then the distro maintainers usually fix it very quickly (if not go find a better distro) and it's fixed for all packages on your system that depend on it. But this doesn't apply to Flatpak where the package providers have to update the libraries in their own package - and the track record isn't great. Sandboxing doesn't help if that vulnerability leads to wiping your home directory.
Even disregarding the trust issues with Flatpak packages made by random people: Packages often contain versions of some libraries in order to not depend on the distro's. If there are security vulnerabilities in a library then the distro maintainers usually fix it very quickly (if not go find a better distro) and it's fixed for all packages on your system that depend on it. But this doesn't apply to Flatpak where the package providers have to update the libraries in their own package - and the track record isn't great. Sandboxing doesn't help if that vulnerability leads to wiping your home directory.