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With your Sapphire Preferred card, you can purchase airline tickets through any travel agency or airline that accepts Visa cards; you are not required to purchase your tickets via the Chase travel portal. You would earn more Ultimate Rewards points per dollar spent if you booked through the Chase portal, but if fares are much higher through the portal, then it will not pay to book there for this particular trip.

If you can get the Skyscanner price by booking directly with the airline, I would suggest that you do so. In the event that something goes wrong with the trip, it is (usually) easier to deal directly with the airline than with a travel agency.