It's about sandboxing your apps... though not every app needs to, or should be sandboxed, but plenty can and should be. I happen to like flatpak a bit more, just feels like a more open community, and appimage is okay as well.

It's about getting dependencies with the app. I can't tell you the number of times I borked my OS install because I wanted a version of a single application that had a feature newer than a year or two old version supported in my distro's repository.

It helps to have both as options.