Superior Rune of the Undead 6 bonus does not convert toughness from sources other than base stats and armor into condition damage.
The rune bonus will consider base toughness, toughness from other runes, and toughness from amulet into the condition damage conversion. However, the rune bonus does not convert toughness from utility skills (Warrior’s Dolyak Signet, Banner of Defence) into condition damage.