Wait so it is a lore/fantasy issue? Or is it a gameplay issue? Because you wrote "I can definitely see myself getting confused or wondering "what was that spell?" in both PVP and PVE content.", meaning that it is a gameplay issue.
Blizzard bypass lore/fantasy issue whenever they want, as we already know, so if that's the nature of the problem (lore/fantasy) they could make everyone happy by adding recolored versions through glyphs and do not care about immersion, as they almost always did in the past.