Flatpak and the containering programs(docker, podman, ...) use the apis of the kernel to prevent access to your files, this is already used by firefox to preven

Flatpak and the containering programs(docker, podman, ...) use the apis of the kernel to prevent access to your files, this is already used by firefox to prevent that javascript accessing data it shouldn't. Additionally SELinux or Apparmor can limit access from services to your files, Android uses SELinux, unprivileged users and binder to isolate apps.