We do a least two international flights a year. Usually each flight has at least two legs, often three.
We also prefer to purchase our tickets direct from the airline. But, sometimes we get a lower price for the same seat, same fare code when we purchase through a third party.
We have never experienced any differences in service, seal allocation, etc when buying from a third party. One international fare purchase was from Orbitz. The fare code was displayed prior to our pushing the buy button. One purchased, we were linked to the airline where we purchased our seats. We tried to book this flight direct but the cost for the same seat, same fare code, was considerably more expensive. Priced within 10 minutes each other. We use matrixit to get prices and fare codes, then we either book with the airline or with third party engine.
Increasingly we find airlines are differentiating their standard economy seat offering into two or even three categories. They use baggage allowances, carry on allowances, and seat selection to differentiate the price. That is even before one gets to the premium economy or business class seat offering.
We are going economy to Athens next week. We had a choice of three prices for economy when booking on the airline web site. One was for carry on, which is what we take, the second was an increase for checked baggage, and a third for seat selection and more baggage. Had we booked through a third party our choices/options would have been the same. These options were identical to the options presented by third party booking sites when we were shopping for fares.
The only difference that we have found when buying airlines seats had nothing whatsoever to do with who we sourced the ticket from. It was all dependent on the ticketed fare code. Anything from full economy to what many would refer to as consolidator class tickets.
We always try to get flight with 2X2 seats. DW likes the window, me the aisle. We sometimes do not sit together so that we can each get our choice of seats. After 40 plus years of marriage and travel we are not bothered about sitting apart for eight or ten hours on a flight.