Our group has also been confused about this - say a boon's check requires Intelligence Arcane. Can you use your Arcane die if it is a "subset" of Charisma (e.g. Seoni), or does it have to be a "subset" of Intelligence?
This sort of question had our group in major confusion the other day.
Similarly, if a check requires Wisdom Divine, and the character has Divine listed under Charisma...?
It's not Intelligence Arcane, it's Intelligence or Arcane.
In your example you can pick Intelligence or Arcane. Then you refer to your character: Do they have the trait you chose? If so use the appropriate die. E.g. you chose the Arcane trait and is playing Seoni. Seoni uses her Charisma die + 2. If you had chosen Intelligence you would use her Intelligence die.