After trying to build mesa with openvg and reverting without it's support, some dangling symbolic files are left in /usr/include/VG that point to non-existent files in /usr/lib64/opengl/xorg-x11/include/VG/*

This made me think about why those headers are installed there in the first place.

It doesn't make sense to package Khronos header files part of mesa, and then to install them all in a folder specific to opengl, which can be misleading as it's only one of the standards. I know right now most openvg implementations rely on opengl, but it wasn't designed that way, and there is already work being done in direct hardware acceleration.

I suggest to package the khronos header files as a separate package from:
http://www.khronos.org/registry/, with maybe a flag to control which standard headers should be copied to the system.

This will avoid also file conflicts on laptops that have different opengl implementations (optimus cards) if any.

I haven't given this solution much thought, so it might not be the right approach to solve this. But changing the use flag on mesa should definitely not lead to broken symbolic files.