EK fills the bulk of it's seats with transit pax (as does EY, but my point is that fares ex-DXB are a small market segment). EK is bigger, has a wider network, and more flights, therefore it's preferred by many people, who are willing to pay a premium (or at least their employers are). Most people in Dubai wouldn't feel it is worth the trek to AUH to save a couple hundred bucks, though some of the fares you quoted are significantly different.

In your case though, doesn't seem to make a lot of sense to fly EK if EY suits you better.