While I wouldn’t want flakpak going deep into the OS I think the advantage of using them on the desktop is obvious. Developers can release to multiple dists from a single build and end users get updates and versions immediately rather than waiting for the dist to update its packages. Plus the ability to lock the software down with sandboxes.

The tradeoff is disk consumption but it’s not really that big of a deal. Flatpaks are layered so apps can share dependencies. e.g. if the app is GNOME it can share the GNOME runtime with other apps and doesn’t need to ship with its own.