Upvote:2
Spehro is quite correct. It will be a combination of cost and allocation. The tours companies will try and of course do the best deals they can with the airline, part of this, in many cases, is a firm commitment to a number of seats on a given flight. If the tour company cannot meet this commitment the airline will shuffle things to get the best yield on each flight (bums on seats at the highest price), or if the tour company is offered and incentive to shift to another - less full flight, they will do so - claiming the airlines wanted it.
All airlines have seat allocations at different pricing - like the $2 airfares, but there may only be 10 seats on any given flight at this fare. A long time industry promotional tool. Using points is the same - there are only a certain number of seats allocated to point based travellers, once these are used up there is no longer availability - even though you may try to book on the same flight to find the plane might be almost empty.
Pointing the finger one way or another in these arrangements is difficult and really doesn't achieve much in the long run as each party will try to shift the accountability to someone else. It does frustrate those of us travelling, but part of the balance between convenience and effort.
We recently did quite an extensive trip on Safari and arranged everything ourselves. It took a little time but we got everything we wanted (flights, accom, tours etc) at a much cheaper rate on our schedule and it was fantastic - I'm lucky my wife loves doing the research - I just turned up. But it can be a fun to do things this way rather than always going with 'all inclusive' tour companies that may not always have our best interests at heart or can be quite restrictive.