The X11 and Wayland compatibility layers are very different than XQuartz macOS or the Wayland-based WSL GUI are, they are much more tightly integrated into Haiku. While you are still going to notice some seams here and there, overall the experience is much more like a "full port" than most other OSes have on this point.
More to the point, all ported applications are still running on top of Haiku's kernel, Haiku's window manager / display server, Haiku's media services, Haiku's init system, Haiku's package manager, etc. On Linux, all those things come from separate projects, and some of them can even be swapped out within a Linux distribution, never mind between distributions. Not so on Haiku.
I hear what you're saying and I do understand the point you're trying to make. However, I think it's interesting to point out just how app-centric systems have become, with many apps even shipping essentially their own unique HIG and look and feel.
If you look at Haiku's competitors, 10 years ago they were all much more editorialized with a strong sense of what a proper, native app for them should look like. And despite all having more such native apps than Haiku has now, the trends have - at least for the time being - pulled away from that. If Haiku gets more popular it'll similarly become subject to simply running the most popular software.
Haiku has its own set of tools.
As long as it's integrated it might avoid Lisp Curse of Linux. It's too easy to fork and too hard to reintegrate.