One quick thought -- Might the lack of refraction through a solid glass orb have been Da Vinci's way of acclaiming that the laws of nature were subservient to the Will of the Divine? Certainly, it would be difficult to assert otherwise, especially given the title of the painting.
I would suggest he intended it to not be glass or an animate object at all instead to be representing and orb of another realm of reality. Scientists can be so narrow minded sometimes. In focusing on it needing to be a physical object they are missing the real genius of his work.
Maybe it represents a particular spherical white stone of ancient that was once in existence in physical form but no longer is but still is, lol. It is neither here nor there. It is in his hand and cannot be removed, taken or stolen. It basically says good luck removing it from its rightful place. It can't be done.