Maybe a more concrete example will answer your question. The Wayland protocols are found here [1]. Your compositor
will implement some of these protocols and not others. If I’m writing an application I will; possibly through some toolkit, ask the compositor what features it supports and configure how my application works accordingly.
This isn’t particularly different to say, an toolkit not supporting a particular form of input, such as GLEW not supporting tablet devices or certain GPU’s having more extension methods — which you can see if you look at Khronos specification. Or an even more drastic example, is an application having both a terminal display and a X11 display like Emacs.