Perhaps I should have been more clear. My apologies. I wanted to draw attention to the fact that -in the case of Fedora Atomic- layering remains a necessity (for most users). This thread goes over it in more detail.

flatpak

Technically speaking, the flatpak format isn't even as limited as some make it out to be. For example, software like Bottles have offered CLI/TUI functionality through it. But Flathub, its most popular storefront, does put a limitation on submissions. Which means that it's effectively not even competing with other package managers that (conventionally) try to offer a broader set of software.

Furthermore, even if the flatpak package exists, not all functionality is retained. For example, the situation around native messaging is still a mess. This prevents e.g. your flatpak browser from communicating with your locally installed password manager. While a(n ugly) workaround exists, it’s quite maddening that it hasn’t been resolved in all these years 😅.

distrobox/toolbx

This is actually a mess. See this comment elsewhere under this post for a bit more elaboration.