This is currently glitched. I unlocked my first God Skill reward and got the corresponding achievement, but after using it in the next mission, nothing popped.
EDIT: As of the 10/10/19 patch, this is now obtainable and thusly the entire game can be completed at 100% finally.
FYI.... you access the God Skill tree in the character menu. Tab all the way over to the end using RB, and there you can use fragments and Gold to unlock upgrades. Also as an aside, you must spend 50 "favor" points in the God Skill tree with one character to unlock the Divine Emissary achievement.