If there is a distinction, and there might be, "completely separate" is exaggerating.
Edit:
I see that only wlroot based implementations are supported so far, and of those there are some things broken in wayfire. Perhaps this is what you're referring to?
The wayland implementation does not support Gnome Shell on wayland (arguably the most mainstream combo since it's the default in ubuntu). To support Gnome Shell on Wayland, you need to include a Gnome Shell extension which has some headaches.
X is a third implementation.
And then there is one additional implementation per Wayland compositor that is not based on wlroots
Not a full and completely separate implementation though. Just wrappers to mask differences in compositor extensions that haven't been stabilized yet. If there are none the implementation is simply impossible.
https://github.com/rvaiya/warpd/tree/master/src/platform/way...
If there is a distinction, and there might be, "completely separate" is exaggerating.
Edit: I see that only wlroot based implementations are supported so far, and of those there are some things broken in wayfire. Perhaps this is what you're referring to?