Good catch! Probably need to have the custom properties on the object, not the world. After all, the object gets linked, not the world.
And if that doesn’t work, then have a look at this post - https://blenderartists.org/t/how-i-rigged-and-animated-color-in-blender/1597825. It describes a method of a custom property on an armature’s bone to control the material. I use the same method to control the brightness of a light attached to a character.
At one point in time, around the blender 2.5 re-write, the motto was “make everything animatable”. Apparently, that vision was lost when it came to linking assets… 
Randy