The point is, it's all self-contained within Flatpak, and won't slow down and pollute your regular package manager when you're doing updates, or say you want to grep some package or whatever. More importantly, fewer dependencies == lesser chances of things breaking. And because it's sandboxed, you don't need to worry too much about having an older library or whatever that's needed to work. And in case you want to uninstall it, it's a fairly clean process, whereas uninstalls via your package manager may not always be clean.