I find this very strange and unique, so you are basically saying that EI accept whatever amount of money that KL or MH decide to give them? And that any web based travel agent can sell tickets for whatever amount they desire?
The web based travel agents can put as much profit on as they want. They're not selling tickets as agents of the airline like the old days but as resellers.
Strangely enough, that isn't the way it works! EI may have pulled themselves off reservation systems such as Amadeus, but they are still the only people that can set fares for their seats! And if KL or MH are selling seats on EI aircraft, then these are at fares set by EI.
Also, you are getting end to end fares that involve another airline, with the bulk of the distance on the other airline - so the biggest element of the fare is down to that airline.
And yet you still continue to blame EI for fares on seats that it's not selling.