I believe I have found a way to acquire third rank Vantus Runes on the rank one quest.

 I defeated Il'gynoth in raid finder and looted the Vantus Rune: Il'gynoth, The Heart of Corruption Rank 1 spell.Upon use I accepted the quest for Vantus Rune Work Order: Il'gynoth, The Heart of Corruption - Quest - World of Warcraft.I created (2) of the Il'gynoth Vantus rune rank 1 instead of (1).Turn in quest to Dalaran Warmage Silva. In my inscription spellbook I have Rank 3 Spell available to learn and no Rank 2.

You know what, this may be intended, I was just reading up on this as I was writing..

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