Since Twilight considers Luna her Mistress instead of the other way around I assume this is an interquel that takes place before chapter 3 of Taking The Sun I?

Twilight still considers Luna to be at the "top of the chain", so to speak, though Twi is so much of a pet as Celestia is. Chapter 3 of part one was intended to confirm to Luna that Twi can handle mistressing Celestia independently, as opposed to actually changing the pecking order.