Linux

The problem is that you can't just convert a deb to rpm or whatever. Well you can and it usually does work, but not always. Tools for that have existed for a long time, and there's plenty of packages in the AUR that just repacks a deb, usually proprietary software, sometimes with bundled hacks to make it run.

There's no guarantee that the libraries of a given distro are at all compatible with the ones of another. For example, Alpine and Void use musl while most others use glibc. These are not binary compatible at all. That deb will never run on Alpine, you need to recompile the whole thing against musl.

What makes a distro a distro is their choice of package manager, the way of handling dependencies, compile flags, package splitting, enabled feature sets, and so on. If everyone used the same binaries for compatibility we wouldn't have distros, we would have a single distro like Windows but open-source but heaven forbid anyone dares switching the compiler flags so it runs 0.5% faster on their brand new CPU.

The Flatpak approach is really more like "fine we'll just ship a whole Fedora-lite base system with the apps". Snaps are similar but they use Ubuntu bases instead (obviously). It's solving a UX problem, using a particular solution, but it's not the solution. It's a nice tool to have so developers can ship a reference environment in which the software is known to run well into and users that just want it to work can use those. But the demand for native packages will never go away, and people will still do it for fun. That's the nature of open-source. It's what makes distros like NixOS, Void, Alpine, Gentoo possible: everyone can try a different way of doing things, for different usecases.

If we can even call it a "problem". It's my distro's job to package the software, not the developer's. That's how distros work, that's what they signed up for by making a distro. To take Alpine again for example, they compile all their packages against musl instead of glibc, and it works great for them. That shouldn't become the developer's problem to care what kind of libc their software is compiled against. Using a Flatpak in this case just bypasses Alpine and musl entirely because it's gonna use glibc from the Fedora base system layer. Are you really running Alpine and musl at that point?

And this is without even touching the different architectures. Some distros were faster to adopt ARM than others for example. Some people run desktop apps on PowerPC like old Macs. Fine you add those to the builds and now someone wants a RISC-V build, and a MIPS build.

There are just way too many possibilities to ever end up with an universal platform that fits everyone's needs. And that's fine, that's precisely why developers ship source code not binaries.