I believe Pkgsrc compiles the program at install, so it’s native. But it’s been a long time since I used it, you might need to look into it.
And you’ll have a hard time finding a “native” package format, because distros have different libraries versions: arch libraries will be much more updated than Debian’s, so things might break trying to execute programs depending on those libraries. That’s why Flatpak, AppImages, Nix, etc bring their own libraries, because if they don’t, things will break.
They are native in the sense that they are Linux executables, but it’s true that they bring their own dependencies, but as I said, that’s necessary for cross distro support.