O&D loads from "___" to DXB are low, so EK gets to jack up prices, and offer the competitive prices to people going beyond DXB.
If you look at QF and compare their price for terminating the journey in DXB, they will be similar or higher, the free market at work.

For people in DXB, looking for a MR, start your journey in MCT and the price drops significantly. Is it convenient , hell no! Does that save you a few thousand AED, once in a while it can.

A good example is:
DXB<>BKK
Compare, EK, EY, GF, QR, TG
TG will be the most expensive, followed by EK, then EY, QR, GF
Look at the trip duration on itamatrix and you will notice that the most efficient flights (aka shorter ) are expensive and the cheapest has long layovers and lousy arrival / departure times.