Just as monkfish aren't actually monks, and bunny cacti aren't actually rabbits (and the Wise Old Man isn't actually wise - Vannaka), 'runite' isn't made of runes. There is no rune essence in its composition. As with most mislabels, it happened a long time ago and has since become common parlance. It's too entrenched to really change it now, regardless of how many times Aubury petitions the Archmage Sedridor.
It's easy to see where the mistake originated from. Runite is a magical metal. When combined with luminite, it develops an aura of resistance. Try to touch the outside of a rune platebody and you will see the problem: it pushes back the hand. That repulsion is handy in battle, when diverting swords and fireballs is handy. It's less handy if you're a platebody cleaner and just want to address some rust.