The rationale for the discounts is that you don't know (or at least it's non-obvious), whether the discount is coming from the flight or the hotel. If the "Book

The rationale for the discounts is that you don't know (or at least it's non-obvious), whether the discount is coming from the flight or the hotel. If the "Book together and save" amount is positive then you'll generally be getting a better deal than direct. You might see the same total price occasionally but it certainly won't be the case the majority of the time.