MamaOO:

I can only speak regarding Kayak cos they’re the ones I use the most. Yes, I have changed fares bought from kayak directly with the airlines. I’ve only used them to fly within the US tho. So I have only changed tickets with US airlines.

Ive also only paid with a USD credit or debit card. The sites I’ve paid with NGN is travelstart. You’re right about these third party sites having lesser fares than the official website, I wonder why that is.

Yes, you are right. A good number of Airlines often have specially reserved in-house packages for them. This is done in a bid to make the industry more competitive and to have a wider reach, sales wise.
Airlines do purposely allow lucrative incentives for 3rd party travel agencies and sister companies to allow for collaborative efforts at reaching travelers better and faster, even at the grassroots level.
If Airlines were to be the only ones selling air travel directly to travelers, their reach may be limited.

Take for instance, an Airline operating a Boeing 747 jumbo jet with capacity for over 700 passengers may take almost forever for all seats to be sold, for a typical route such as from Lagos (LOS) to Heathrow London (LON). This may cause unnecessary delays and inability for the Airline to meet up with official flight schedules, except it wants to travel with several hundreds of empty seats. A huge economic loss that will be.

However, by giving room to competitiveness and not being too greedy by creating some channels of profitability for travel agencies all over the place, it is easy to quickly sell out all seats and thereby meet schedules, and profitably too.

Such well established giant travel agencies as WakaNow and TravelStart benefit from the hidden in-house offers that Airlines make available from time to time.

The beauty of this sort of business model is that the travel agencies are able to weigh (compare) various existing offers, fares and rates from hundreds or thousands of Airlines that they are affiliated to and therefore present their customers and indeed members of the traveling public the most affordable and mouth watering deals often better than what any traveler may be able to directly get from the Airlines themselves.