Flatpak’s benefits mostly exist for the developer. Apt is more tightly integrated with the distro, which is generally advantageous, but also means more work for packaging. Flatpak’s benefit is that it’s a compatibility layer for lots of different distros. In a perfect world, every distro would have a large library of packages in the official repo, but that’s a lot of work for devs, and flatpak lets them avoid that sprawling support.