On X11, where there is a high-level “full screen window” concept, GLFW will tell the window manager to treat a mode 4 window as full screen for the chosen monitor. From that point the window manager takes care of things like placement, z-order, compositor bypassing and possibly other things. GLFW also supports the separate mechanism specifically for asking a window manager to bypass compositing and will apply it to mode 4 windows but not mode 3 ones.
On macOS we don’t yet but will support optionally giving mode 4 windows their own Spaces, which is another (weirder) kind of high-level full screen window concept.
A mode 3 window (if you also make it topmost but leave out maximization) and a mode 4 window will likely be treated the same wrt compositing on Windows. OpenGL compositor bypassing on Windows is controlled by the GPU driver, which as far as I can tell will ignore the hints available for this and instead decide ad-hoc based on the placement and style flags of the window. These will look pretty similar for modes 3 and 4 since Windows doesn’t have a real full screen concept.