the NVIDIA driver still needs NVIDIA GLX and GL libraries in order for OpenGL to work.
The intention is to avoid clobbering existing GL/GLX libraries (such as Mesa/Gallium3D) that might be needed for a different (non-NVIDIA) GPU. This can be useful in settings where the NVIDIA GPU is not used for graphics at all. For example, using an NVIDIA GPU for CUDA/OpenCL on a system which already has a different GPU that is being used for graphics, including OpenGL.
Yes, if you want to install the NVIDIA GL libraries, but avoid conflict with an existing GL implementation, the --opengl-prefix flag works fine for that. This option isn't for that, though; it's for avoiding installation of GL libraries completely when they're not needed at all.