I like flatpak because it keeps everything more orderly. My OS fits into one box, and my userland applications all get their own little box. I don’t have to worry about the choices I make for my OS dictating the options I have for applications. And I don’t have to worry about installing an application polluting my OS with libraries that only it will ever use.
The same is true with containers like Docker. Sure, I could install web apps directly on the server, or make a VM for every service I wanted to spool up, but with Docker Config(or the many other ways to wrangle docker) I have a predictable input/output. I never have to worry about the requirements of one service conflicting with another. And the data and logs generated by the service rest in an exact place that I can ensure is uniform for all services, even if the developers do wacky things.
Taken to the extreme you get NixOS, which I really like the concept of, but can’t bring myself around to learning, as I know it will take over my life.