Superior runes 12/6??
If you take one off, does it go to 11/6?
So I simply cannot answer with yes so here’s a lengthy one.
Well that sounds like a bug to me. A quick search found this:
One is that the item UI displays rune set bonuses as cumulative across both the player’s PvE and PvP equipment (thus why it shows 12/6 instead of 6/6). However, the attribute bonuses themselves are applied based on how many runes are equipped to your currently equipped armor set, so while it may look incorrect, your character should have the correct attribute bonuses from both sets.