Yeah, that's what I mean. You can use flatpak (or snap if you swing that way) but you can also install applications via containers. They're still not installed on the OS-- even "native" applications get installed via the container. So if the application you want is maintained for arch in aur, you can add the --aur tag to the apx command and it will install that version instead of the default, which is ubuntu. This also works for fedora applications.
Edit: More info here: https://handbook.vanillaos.org/2023/01/11/install-and-manage-applications.html
I'm sure it does to some degree, though I don't know if it's enough to matter on modern computers, and isn't that what flatpak does, too? (duplicating dependencies)
In any event, if you don't need an application from a specific distro there's no reason to create that container. The non-ubuntu ones get created when they're needed. (And I think the next version of VanillaOS will be debian-based, not ubuntu; in case that matters.)